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Complete EZview reformatting

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This commit is contained in:
Bryan Roessler
2024-07-31 00:36:40 -04:00
parent 79e3676ed3
commit 019fb07f79
36 changed files with 7526 additions and 8544 deletions
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1
workflow/apps/matlab/easy/EASYconsole.m
View File

@@ -40,7 +40,6 @@ function varargout = EASYconsole(varargin)
fprintf('This script name: %s\n', easyFileName);
% Set scansDir (project scans directory) intelligently
if exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
scansDir=fullfile(getenv('PROJECT_SCANS_DIR'));
if exist(scansDir, 'dir')

144
workflow/apps/matlab/ezview/EZRFs4DayComp.m
View File

@@ -1,12 +1,11 @@
%EZRFs4DayComp Called by EZmDayComp.m
%For this multiDay Exp series the actual perturbation being studied is
%Aging as related in the time series experiment i.e.,(nn) or DexpN
%That is holding the DrugMedia pert constant(at the DM slider number) and plotting
RFconfig= Exp(zoneSel).Dexp(DexpN).RFconfig;
RFsel= Exp(zoneSel).htmapRFanswer;
j= pertSel; m= MPsel;
% EZRFs4DayComp Called by EZmDayComp.m
% For this multiDay Exp series the actual perturbation being studied is
% Aging as related in the time series experiment i.e.,(nn) or DexpN
% That is holding the DrugMedia pert constant(at the DM slider number) and plotting
RFconfig=Exp(zoneSel).Dexp(DexpN).RFconfig;
RFsel=Exp(zoneSel).htmapRFanswer;
j=pertSel; m=MPsel;
if RFconfig==1
try
RF1mdIndx(nn)=Exp(zoneSel).Dexp(nn).RFmd1indx(pertSel);
RF1mdPltN(nn)=Exp(zoneSel).Dexp(nn).RFmd1pltN; %This is the MP number for RF1
@@ -15,65 +14,62 @@ if RFconfig==1
try
RF2mdIndx(nn)=Exp(zoneSel).Dexp(nn).RFmd2indx(pertSel);
RF2mdPltN(nn)=Exp(zoneSel).Dexp(nn).RFmd2pltN;
%special case for 'RFmd2val' See Calc. at EZmDayComp ~ln139
% special case for 'RFmd2val' See Calc. at EZmDayComp ~ln139
catch, end
try Rn(nn)=Exp(expN).Dexp(nn).RFmean(pertSel); catch, Rn(nn)=0; end
try Rs(nn)=Exp(expN).Dexp(nn).RFstd(pertSel); catch, Rs(nn)=0; end
end
if RFconfig==2
ctrlRF= RFsel{1};
ctrlRF=RFsel{1};
j=pertSel; m=MPsel;
switch ctrlRF
case {'G','g'}
%Set to (nn) day as these median values are being plotted directly
RFmdIndx(nn)= Exp(zoneSel).Dexp(nn).RFmdGindx(pertSel);
RFmdPltN(nn)= Exp(zoneSel).Dexp(nn).RFmdGpltN(pertSel); %G could have a different MP for each DM;At any rate it is stored for each DM regardless.
RFmdVal(nn)= Exp(zoneSel).Dexp(nn).RFmedianG(pertSel);
%Set mean values to Day 1 as these are used in Interaction Calc.
%as the first reference ctrlRF 'Aging Perturbation'
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(pertSel);
% Set to (nn) day as these median values are being plotted directly
RFmdIndx(nn)=Exp(zoneSel).Dexp(nn).RFmdGindx(pertSel);
RFmdPltN(nn)=Exp(zoneSel).Dexp(nn).RFmdGpltN(pertSel); %G could have a different MP for each DM;At any rate it is stored for each DM regardless.
RFmdVal(nn)=Exp(zoneSel).Dexp(nn).RFmedianG(pertSel);
% Set mean values to Day 1 as these are used in Interaction Calc.
% as the first reference ctrlRF 'Aging Perturbation'
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(pertSel);
case {'L','l'}
%Set to (nn) day as these median values are being plotted directly
RFmdVal(nn)= Exp(zoneSel).Dexp(nn).RFmedianP(pertSel);
%Set mean values to Day 1 as these are used in Interaction Calc.
%as the first reference ctrlRF 'Aging Perturbation'
% Set to (nn) day as these median values are being plotted directly
RFmdVal(nn)=Exp(zoneSel).Dexp(nn).RFmedianP(pertSel);
% Set mean values to Day 1 as these are used in Interaction Calc.
% as the first reference ctrlRF 'Aging Perturbation'
if Exp(expN).Dexp(nn).meanP(j,m)~=0
Rn(nn)= Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)= Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0||isempty(Exp(expN).Dexp(nn).meanP(j,m)) &&...
strcmpi(ctrlRF,'G')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(pertSel);
Rn(nn)=Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)=Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0||isempty(Exp(expN).Dexp(nn).meanP(j,m)) ...
&& strcmpi(ctrlRF,'G')
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(pertSel);
end
end
pertRF= RFsel{2}; %These results are only used for N2 future Interaction Calc.
%nn is ordered number of the selected chronological day Experiment
%In the chronological study, Age (day sequence results) is the
%'Perturbation' of interest instead of DrugMedia concentration.
pertRF=RFsel{2}; % These results are only used for N2 future Interaction Calc.
% nn is ordered number of the selected chronological day Experiment
% In the chronological study, Age (day sequence results) is the
% 'Perturbation' of interest instead of DrugMedia concentration.
switch pertRF
case {'G','g'}
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(pertSel);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(pertSel);
case {'L','l'}
j= pertSel; m= MPsel;
j=pertSel; m=MPsel;
if Exp(expN).Dexp(nn).meanP(j,m)~=0
Rn(nn)= Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)= Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0||isempty(Exp(expN).Dexp(nn).meanP(j,m)) &&...
strcmpi(ctrlRF,'G')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(j);
Rn(nn)=Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)=Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0||isempty(Exp(expN).Dexp(nn).meanP(j,m)) ...
&& strcmpi(ctrlRF,'G')
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(j);
end
end
end
if RFconfig==3
j= pertSel; m= MPsel;
ctrlRF= RFsel{1};
j=pertSel; m=MPsel;
ctrlRF=RFsel{1};
switch ctrlRF
case {'F','f'}
@@ -89,49 +85,49 @@ if RFconfig==3
catch, end
try Rn(nn)=Exp(expN).Dexp(nn).RFmean; catch, Rn(nn)=0; end
try Rs(nn)=Exp(expN).Dexp(nn).RFstd; catch, Rs(nn)=0; end
Rn(nn)= Exp(expN).Dexp(nn).RFmean(nn);
Rs(nn)= Exp(expN).Dexp(nn).RFstd(nn);
Rn(nn)=Exp(expN).Dexp(nn).RFmean(nn);
Rs(nn)=Exp(expN).Dexp(nn).RFstd(nn);
case {'G','g'}
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(nn);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(nn);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(nn);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(nn);
case {'L','l'}
Rn(nn)= Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)= Exp(expN).Dexp(nn).stdP(j,m);
if Exp(expN).Dexp(nn).meanP(j,m)~=0,
Rn(nn)= Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)= Exp(expN).Dexp(nn).stdP(j,m);
Rn(nn)=Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)=Exp(expN).Dexp(nn).stdP(j,m);
if Exp(expN).Dexp(nn).meanP(j,m)~=0
Rn(nn)=Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)=Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0 && strcmpi(ctrlRF,'G')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(j);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(j);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0 && strcmpi(ctrlRF,'F')
Rn(nn)= Exp(expN).Dexp(nn).RFmean(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstd(j);
Rn(nn)=Exp(expN).Dexp(nn).RFmean(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstd(j);
elseif Exp(expN).Dexp(nn).meanP(1,m)==0 && strcmpi(ctrlRF,'L')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(1);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(1);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(1);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(1);
end
end
pertRF= RFsel{2};
pertRF=RFsel{2};
switch pertRF
case {'F','f'}
Rn(nn)= Exp(expN).Dexp(nn).RFmean(pertSel);
Rs(nn)= Exp(expN).Dexp(nn).RFstd(pertSel);
Rn(nn)=Exp(expN).Dexp(nn).RFmean(pertSel);
Rs(nn)=Exp(expN).Dexp(nn).RFstd(pertSel);
case {'G','g'}
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(pertSel);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(pertSel);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(pertSel);
case {'L','l'}
if Exp(expN).Dexp(nn).meanP(j,m)~=0,
Rn(nn)= Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)= Exp(expN).Dexp(nn).stdP(j,m);
Rn(nn)=Exp(expN).Dexp(nn).meanP(j,m);
Rs(nn)=Exp(expN).Dexp(nn).stdP(j,m);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0 && strcmpi(ctrlRF,'G')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(j);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(j);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0 && strcmpi(ctrlRF,'F')
Rn(nn)= Exp(expN).Dexp(nn).RFmean(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstd(j);
Rn(nn)=Exp(expN).Dexp(nn).RFmean(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstd(j);
elseif Exp(expN).Dexp(nn).meanP(j,m)==0 && strcmpi(ctrlRF,'L')
Rn(nn)= Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)= Exp(expN).Dexp(nn).RFstdG(j);
Rn(nn)=Exp(expN).Dexp(nn).RFmeanG(j);
Rs(nn)=Exp(expN).Dexp(nn).RFstdG(j);
end
end
end

202
workflow/apps/matlab/ezview/EZVimDisplay.m
View File

@@ -1,48 +1,44 @@
%ImageDisplay
% ImageDisplay
global Exp
global ghandles
global zonePB
prntHt=0;
%Test for Bad MP cell array (usually 384 [NaN}'s)
%replaced length(Exp(expN).Dexp(1).MP) with MPnum
for mx=1:length(Exp(expN).Dexp(1).MP)
% Test for Bad MP cell array (usually 384 [NaN}'s)
% replaced length(Exp(expN).Dexp(1).MP) with MPnum
for mx=1:length(Exp(expN).Dexp(1).MP)
try
char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))
MPnum=mx;
catch
break
end
end
%*************************************************
end
if expN==1,DexpN= (get(handles.DN1,'value')); end
if expN==2,DexpN= (get(handles.DN2,'value')); end
if expN==3,DexpN= (get(handles.DN3,'value')); end
Exp(expN).DexpN=DexpN;
if strcmp(Exp(expN).DexpType,'single'),
if expN==1,DexpN=(get(handles.DN1,'value')); end
if expN==2,DexpN=(get(handles.DN2,'value')); end
if expN==3,DexpN=(get(handles.DN3,'value')); end
Exp(expN).DexpN=DexpN;
if strcmp(Exp(expN).DexpType,'single')
DexpN=1;
elseif ~strcmp(Exp(expN).DexpType,'single')
if expN==1
set(handles.MPsldr1,'min',1,'max',MPnum)
DMnum= length(Exp(expN).Dexp(DexpN).DM.drug);
DMnum=length(Exp(expN).Dexp(DexpN).DM.drug);
set(handles.DMsldr1,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr1,'min',1,'max',tPtsSize)
end
if expN==2
set(handles.MPsldr2,'min',1,'max',MPnum)
DMnum= length(Exp(expN).Dexp(DexpN).DM.drug);
DMnum=length(Exp(expN).Dexp(DexpN).DM.drug);
set(handles.DMsldr2,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr2,'min',1,'max',tPtsSize)
end
if expN==3
set(handles.MPsldr3,'min',1,'max',MPnum)
DMnum= length(Exp(expN).Dexp(DexpN).DM.drug);
DMnum=length(Exp(expN).Dexp(DexpN).DM.drug);
set(handles.DMsldr3,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr3,'min',1,'max',tPtsSize)
@@ -50,153 +46,141 @@ elseif ~strcmp(Exp(expN).DexpType,'single')
end
ghandles=handles;
scan=Exp(expN).Dexp(DexpN).scan;
destPerMP= length(Exp(expN).Dexp(DexpN).DM.drug);
scan=Exp(expN).Dexp(DexpN).scan;
destPerMP=length(Exp(expN).Dexp(DexpN).DM.drug);
if expN==1,MPsel=floor(get(handles.MPsldr1,'value')); end
if expN==2,MPsel=floor(get(handles.MPsldr2,'value')); end
if expN==3,MPsel=floor(get(handles.MPsldr3,'value')); end
if expN==1,pertSel=floor(get(handles.DMsldr1,'value')); end
if expN==2,pertSel=floor(get(handles.DMsldr2,'value')); end
if expN==3,pertSel=floor(get(handles.DMsldr3,'value')); end
if expN==1,tPtSel=floor(get(handles.Tptsldr1,'value')); end
if expN==2,tPtSel=floor(get(handles.Tptsldr2,'value')); end
if expN==3,tPtSel=floor(get(handles.Tptsldr3,'value')); end
plateNum= (MPsel-1)*destPerMP + pertSel;
tPtsSize=[];
tPtsSize= length(Exp(expN).Dexp(DexpN).scan(plateNum).plate(1).tSeries(:))
if expN==1,MPsel=floor(get(handles.MPsldr1,'value')); end
if expN==2,MPsel=floor(get(handles.MPsldr2,'value')); end
if expN==3,MPsel=floor(get(handles.MPsldr3,'value')); end
if expN==1,pertSel=floor(get(handles.DMsldr1,'value')); end
if expN==2,pertSel=floor(get(handles.DMsldr2,'value')); end
if expN==3,pertSel=floor(get(handles.DMsldr3,'value')); end
if expN==1,tPtSel=floor(get(handles.Tptsldr1,'value')); end
if expN==2,tPtSel=floor(get(handles.Tptsldr2,'value')); end
if expN==3,tPtSel=floor(get(handles.Tptsldr3,'value')); end
plateNum=(MPsel-1)*destPerMP + pertSel;
tPtsSize=[];
tPtsSize=length(Exp(expN).Dexp(DexpN).scan(plateNum).plate(1).tSeries(:))
n=1;
for ii= 1:tPtsSize
for ii=1:tPtsSize
if exist(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat((num2str(ii)),'.bmp'))) ==2; %the .bmp file exists
bmpLst(n)= ii
bmpLst(n)=ii
n=n+1
end
end
if tPtSel> tPtsSize
tPtSel= tPtsSize
end
if exist(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat((num2str(tPtSel)),'.bmp'))) ==0; %the .bmp file exists
tPtSel= bmpLst(find(bmpLst>tPtSel,1,'first'))
tPtSel=tPtsSize
end
if expN==1,
if exist(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat((num2str(tPtSel)),'.bmp'))) ==0; %the .bmp file exists
tPtSel=bmpLst(find(bmpLst>tPtSel,1,'first'))
end
if expN==1,
set(handles.Tptsldr1,'max',tPtsSize);
set(ghandles.Tptsldr1,'max',tPtsSize);
set(handles.Tpted1,'string', num2str(tPtSel));
set(ghandles.Tpted1,'string', num2str(tPtSel));
if tPtsSize<= tPtSel,
if tPtsSize<=tPtSel,
set(handles.Tptsldr1,'value', tPtsSize)
set(ghandles.Tptsldr1,'value', tPtsSize)
tPtSel= tPtsSize
tPtSel=tPtsSize
set(handles.Tpted1,'string', num2str(tPtsSize))
set(ghandles.Tpted1,'string', num2str(tPtsSize))
end
end
if expN==2
end
if expN==2
set(handles.Tptsldr2,'max',tPtsSize);
set(ghandles.Tptsldr2,'max',tPtsSize);
set(handles.Tpted2,'string', num2str(tPtSel));
set(ghandles.Tpted2,'string', num2str(tPtSel));
if tPtsSize<= tPtSel,
if tPtsSize<=tPtSel,
set(handles.Tptsldr2,'value', tPtsSize)
set(ghandles.Tptsldr2,'value', tPtsSize)
tPtSel= tPtsSize
tPtSel=tPtsSize
set(handles.Tpted2,'string', num2str(tPtsSize))
set(ghandles.Tpted2,'string', num2str(tPtsSize))
end
end
if expN==3
end
if expN==3
set(handles.Tptsldr3,'max',tPtsSize);
set(ghandles.Tptsldr3,'max',tPtsSize);
set(handles.Tpted3,'string', num2str(tPtSel));
set(ghandles.Tpted3,'string', num2str(tPtSel));
if tPtsSize<= tPtSel,
if tPtsSize<=tPtSel,
set(handles.Tptsldr3,'value', tPtsSize)
set(ghandles.Tptsldr3,'value', tPtsSize)
tPtSel= tPtsSize
tPtSel=tPtsSize
set(handles.Tpted3,'string', num2str(tPtsSize))
set(ghandles.Tpted3,'string', num2str(tPtsSize))
end
end
end
%---------------------------------------------------------
Exp(expN).Dexp(DexpN).MPsel=MPsel;
Exp(expN).Dexp(DexpN).destPerMP=destPerMP;
Exp(expN).Dexp(DexpN).pertSel=pertSel;
Exp(expN).Dexp(DexpN).tPtSel=tPtSel;
Exp(expN).Dexp(DexpN).plateNum=plateNum;
%try
I=imread(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat(num2str(tPtSel),'.bmp')));
Exp(expN).Dexp(DexpN).MPsel=MPsel;
Exp(expN).Dexp(DexpN).destPerMP=destPerMP;
Exp(expN).Dexp(DexpN).pertSel=pertSel;
Exp(expN).Dexp(DexpN).tPtSel=tPtSel;
Exp(expN).Dexp(DexpN).plateNum=plateNum;
%try
I= imread(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat(num2str(tPtSel),'.bmp')));
%set(ghandles.Iaxes1,'CurrentAxes')
if expN==1, expAxes=ghandles.Iaxes1;end
if expN==2, expAxes=ghandles.Iaxes2;end
if expN==3, expAxes=ghandles.Iaxes3;end
axes(expAxes)
imshow(I)
set(expAxes,'xtick',[],'ytick',[])
%set(ghandles.Iaxes1,'CurrentAxes')
if expN==1, expAxes=ghandles.Iaxes1;end
if expN==2, expAxes=ghandles.Iaxes2;end
if expN==3, expAxes=ghandles.Iaxes3;end
DMstr=char(strcat('Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ', ...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ', ...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ', ...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}))
axes(expAxes)
imshow(I)
set(expAxes,'xtick',[],'ytick',[])
if expN==1,set(handles.DM1,'string',DMstr); end
if expN==2,set(handles.DM2,'string',DMstr); end
if expN==3,set(handles.DM3,'string',DMstr); end
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
if expN==1,set(handles.tptTm1,'string',tPtStr); end
if expN==2,set(handles.tptTm2,'string',tPtStr); end
if expN==3,set(handles.tptTm3,'string',tPtStr); end
DMstr= char(strcat('Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}))
if expN==1,set(handles.DM1,'string',DMstr); end
if expN==2,set(handles.DM2,'string',DMstr); end
if expN==3,set(handles.DM3,'string',DMstr); end
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
if expN==1,set(handles.tptTm1,'string',tPtStr); end
if expN==2,set(handles.tptTm2,'string',tPtStr); end
if expN==3,set(handles.tptTm3,'string',tPtStr); end
xp=char(Exp(expN).Dexp(DexpN).resDir);
if ispc
xp=char(Exp(expN).Dexp(DexpN).resDir);
if ispc
slashPos=strfind(char(Exp(expN).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(expN).Dexp(DexpN).resDir),'/');
end
startPos=slashPos(length(slashPos)-2) +1;
endPos=(slashPos(length(slashPos)) -1);
expStrg= xp(startPos:end);
end
if expN==1,set(handles.expName1,'string',expStrg); end
if expN==2,set(handles.expName2,'string',expStrg); end
if expN==3,set(handles.expName3,'string',expStrg); end
startPos=slashPos(length(slashPos)-2) +1;
endPos=(slashPos(length(slashPos)) -1);
expStrg=xp(startPos:end);
if expN==1,set(handles.expName1,'string',expStrg); end
if expN==2,set(handles.expName2,'string',expStrg); end
if expN==3,set(handles.expName3,'string',expStrg); end
%********************
try
try
htMapTogPBfg=0;
EZhtMap %
catch
end
%********************
EZhtMap
catch
end
%********************************************************************
%zonePB handle control from left graph spot side to communicate to right side 23_0818
%This section was based on the zoneRad Section for Radiobuttons which were
%unusable with the new form of Radio Buttons in AppDesigner.
%********************
% zonePB handle control from left graph spot side to communicate to right side 23_0818
% This section was based on the zoneRad Section for Radiobuttons which were
% unusable with the new form of Radio Buttons in AppDesigner.
if expN==1
zonesel=1;
zonePB= 1;
zonePB=1;
set(handles. zonePB1,'value',1)
set(handles. zonePB2,'value',0)
set(handles. zonePB3,'value',0)
set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6])
set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0])
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
orfLstSel=get(handles.GeneOrfTog,'value');
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(1).Dexp(DexpN).srtOrfLst)
@@ -207,14 +191,13 @@ end
if expN==2
zonesel=2;
zonePB= 2;
zonePB=2;
set(handles. zonePB2,'value',1)
set(handles. zonePB1,'value',0)
set(handles. zonePB3,'value',0)
set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6])
set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0])
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
orfLstSel=get(handles.GeneOrfTog,'value');
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(2).Dexp(DexpN).srtOrfLst)
@@ -225,14 +208,13 @@ end
if expN==3
zonesel=3;
zonePB= 3;
zonePB=3;
set(handles. zonePB3,'value',1)
set(handles. zonePB2,'value',0)
set(handles. zonePB1,'value',0)
set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
orfLstSel=get(handles.GeneOrfTog,'value');
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(3).Dexp(DexpN).srtOrfLst)

157
workflow/apps/matlab/ezview/EZcompositePlot.m
View File

@@ -2,128 +2,121 @@
global Exp
global ghandles
if (Exp(expN).cTraceN>1 && length(Exp(expN).ll)<= (Exp(expN).cTraceIndx((Exp(expN).cTraceN)))) ||...
isempty(Exp(expN).ll)
return;
if (Exp(expN).cTraceN>1 && length(Exp(expN).ll)<=(Exp(expN).cTraceIndx((Exp(expN).cTraceN)))) ||...
isempty(Exp(expN).ll)
return;
end
Exp(expN).CompositPlot=1;
if expN==1, OLaxes=ghandles.OLaxes1; end
if expN==2, OLaxes=ghandles.OLaxes2; end
if expN==3, OLaxes=ghandles.OLaxes3; end
if expN==1, OLaxes=ghandles.OLaxes1; end
if expN==2, OLaxes=ghandles.OLaxes2; end
if expN==3, OLaxes=ghandles.OLaxes3; end
cTraceN= mod(Exp(expN).cTraceN,10);
%cTraceN= Exp(expN).cTraceN;
if cTraceN==1, colour= 'b';
elseif cTraceN==2, colour= 'g';
elseif cTraceN==3, colour= 'r';
elseif cTraceN==4, colour= 'c';
elseif cTraceN==5, colour= 'm';
elseif cTraceN==6, colour= 'b';
elseif cTraceN==7, colour= 'g';
elseif cTraceN==8, colour= 'r';
elseif cTraceN==9, colour= 'c';
elseif cTraceN==0, colour= 'm';
cTraceN=mod(Exp(expN).cTraceN,10);
%cTraceN=Exp(expN).cTraceN;
if cTraceN==1, colour='b';
elseif cTraceN==2, colour='g';
elseif cTraceN==3, colour='r';
elseif cTraceN==4, colour='c';
elseif cTraceN==5, colour='m';
elseif cTraceN==6, colour='b';
elseif cTraceN==7, colour='g';
elseif cTraceN==8, colour='r';
elseif cTraceN==9, colour='c';
elseif cTraceN==0, colour='m';
end
AddCplot=1; %Test need for user question dialog boxS
if AddCplot==1,
cTraceN= Exp(expN).cTraceN
cTraceIndx= Exp(expN).cTraceIndx(cTraceN)
cTstart= cTraceIndx;
cTend= length(Exp(expN).ll);
cTraceN=Exp(expN).cTraceN
cTraceIndx=Exp(expN).cTraceIndx(cTraceN)
cTstart=cTraceIndx;
cTend=length(Exp(expN).ll);
jj= 0; ii=0; RFcmpTraces=0; maxRFcmpLStd=0; maxRFcmpKStd=0; maxRFcmprStd= 0;
for ic= cTstart:cTend
jj=0; ii=0; RFcmpTraces=0; maxRFcmpLStd=0; maxRFcmpKStd=0; maxRFcmprStd=0;
for ic=cTstart:cTend
if strcmp(get(Exp(expN).hOL(ic),'visible'), 'on')
jj= jj+1;
mlstL(jj)= Exp(expN).ll(ic); mlstR(jj)= Exp(expN).rr(ic); mlstK(jj)= Exp(expN).kk(ic);
LBcheck= char(Exp(expN).hOLname(ic))
jj=jj+1;
mlstL(jj)=Exp(expN).ll(ic); mlstR(jj)=Exp(expN).rr(ic); mlstK(jj)=Exp(expN).kk(ic);
LBcheck=char(Exp(expN).hOLname(ic))
if isequal(LBcheck(4:6),'cmp'),
if Exp(expN).lstd(ic)> maxRFcmpLStd
maxRFcmpLStd= Exp(expN).lstd(ic);
maxRFcmpLStd=Exp(expN).lstd(ic);
ii=ii+1;
lstds(ii)= Exp(expN).lstd(ic);
lstds(ii)=Exp(expN).lstd(ic);
RFcmpTraces(ii)=ic;
end
if Exp(expN).kstd(ic)> maxRFcmpKStd
maxRFcmpKStd= Exp(expN).kstd(ic);
maxRFcmpKStd=Exp(expN).kstd(ic);
end
if Exp(expN).rstd(ic)> maxRFcmprStd
maxRFcmprStd= Exp(expN).rstd(ic);
maxRFcmprStd=Exp(expN).rstd(ic);
end
end
end
end
end
%for n= 1:length(RFcmpTraces +1)
%end
maxLstd= max(std(mlstL), maxRFcmpLStd);
maxKstd= max(std(mlstK), maxRFcmpKStd);
maxrstd= max(std(mlstR), maxRFcmprStd);
Exp(expN).cLmean(cTraceN)= mean(mlstL); Exp(expN).cLstd(cTraceN)= maxLstd;
Exp(expN).cRmean(cTraceN)= mean(mlstR); Exp(expN).cKstd(cTraceN)= maxKstd; %std(mlstR);
Exp(expN).cKmean(cTraceN)= mean(mlstK); Exp(expN).cRstd(cTraceN)= maxrstd; %std(mlstK);
end
maxLstd=max(std(mlstL), maxRFcmpLStd);
maxKstd=max(std(mlstK), maxRFcmpKStd);
maxrstd=max(std(mlstR), maxRFcmprStd);
Exp(expN).cLmean(cTraceN)=mean(mlstL); Exp(expN).cLstd(cTraceN)=maxLstd;
Exp(expN).cRmean(cTraceN)=mean(mlstR); Exp(expN).cKstd(cTraceN)=maxKstd; %std(mlstR);
Exp(expN).cKmean(cTraceN)=mean(mlstK); Exp(expN).cRstd(cTraceN)=maxrstd; %std(mlstK);
%******MEAN calculation Plot********************
%try
l=Exp(expN).cLmean(cTraceN);
r=Exp(expN).cRmean(cTraceN);
K=Exp(expN).cKmean(cTraceN);
lslow=l + Exp(expN).cLstd(cTraceN); lfast= l - Exp(expN).cLstd(cTraceN);
rl=r - Exp(expN).cRstd(cTraceN); ru= r + Exp(expN).cRstd(cTraceN);
Kl=K - Exp(expN).cKstd(cTraceN); Ku= K + Exp(expN).cKstd(cTraceN);
clear g;
t=1:200;
g=K ./ (1 + exp(-r.* (t - l )));
% Mean calculation plot
l=Exp(expN).cLmean(cTraceN);
r=Exp(expN).cRmean(cTraceN);
K=Exp(expN).cKmean(cTraceN);
lslow=l + Exp(expN).cLstd(cTraceN); lfast=l - Exp(expN).cLstd(cTraceN);
rl=r - Exp(expN).cRstd(cTraceN); ru=r + Exp(expN).cRstd(cTraceN);
Kl=K - Exp(expN).cKstd(cTraceN); Ku=K + Exp(expN).cKstd(cTraceN);
clear g;
t=1:200;
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
if K==0||r==0||l==0
g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;
end
Exp(expN).hCmean(cTraceN)=plot(OLaxes,t,g);hold on; %PLOT the composit mean of traces
Exp(expN).hBound1(cTraceN)= plot(OLaxes,t,gSlow,'y');
Exp(expN).hBound2(cTraceN)= plot(OLaxes,t,gFast,'y');
%c1= c1-((cTraceN-1)*0.2); c2= c2+((cTraceN-1)*0.2); c3= c3+((cTraceN-1)*0.2);
Exp(expN).hCmean(cTraceN)=plot(OLaxes,t,g);hold on; % plot the composit mean of traces
Exp(expN).hBound1(cTraceN)=plot(OLaxes,t,gSlow,'y');
Exp(expN).hBound2(cTraceN)=plot(OLaxes,t,gFast,'y');
%c1=c1-((cTraceN-1)*0.2); c2=c2+((cTraceN-1)*0.2); c3=c3+((cTraceN-1)*0.2);
set(Exp(expN).hCmean(cTraceN),'color',colour) %[c1 c2 c3]) %Set latest trace red
set(Exp(expN).hCmean(cTraceN),'linewidth',3)
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Lstr= num2str(Exp(expN).cLmean(cTraceN)); Lsstr= num2str(Exp(expN).cLstd(cTraceN));
Rstr= num2str(Exp(expN).cRmean(cTraceN)); Rsstr= num2str(Exp(expN).cRstd(cTraceN));
Kstr= num2str(Exp(expN).cKmean(cTraceN)); Ksstr= num2str(Exp(expN).cKstd(cTraceN));
Lstr=num2str(Exp(expN).cLmean(cTraceN)); Lsstr=num2str(Exp(expN).cLstd(cTraceN));
Rstr=num2str(Exp(expN).cRmean(cTraceN)); Rsstr=num2str(Exp(expN).cRstd(cTraceN));
Kstr=num2str(Exp(expN).cKmean(cTraceN)); Ksstr=num2str(Exp(expN).cKstd(cTraceN));
try
cPlotLB= strcat('Composite', num2str(cTraceN),'->','L=',Lstr(1:4),';','Ls=',Lsstr(1:4),';',...
cPlotLB=strcat('Composite', num2str(cTraceN),'->','L=',Lstr(1:4),';','Ls=',Lsstr(1:4),';',...
'r=',Rstr(1:4),';','rs=',Rsstr(2:6),';','K=',Kstr(1:4),';','Ks=',Ksstr(1:4))
catch
try cPlotLB= strcat('Composite', num2str(cTraceN),'->','L=',Lstr(1:4),';','r=',Rstr(1:4),';','K=',Kstr(1:4),'-SingleSource'); catch, end
try
cPlotLB=strcat('Composite', num2str(cTraceN),'->','L=',Lstr(1:4),';','r=',Rstr(1:4),';','K=',Kstr(1:4),'-SingleSource');
catch
end
end
%}
Exp(expN).cName(cTraceN)= {cPlotLB};
Exp(expN).cName(cTraceN)={cPlotLB};
if expN==1, set(ghandles.OLay1,'string', cPlotLB); end
if expN==2, set(ghandles.OLay2,'string', cPlotLB); end
if expN==3, set(ghandles.OLay3,'string', cPlotLB); end
%Hide source traces leaving only the Composite traces and STD traces
for i= 1:length(Exp(expN).hOL)
% Hide source traces leaving only the Composite traces and STD traces
for i=1:length(Exp(expN).hOL)
set(Exp(expN).hOL(i),'Visible','off')
try set(Exp(expN).hOLb(i),'Visible','off'); catch, msg= 'No raw data RFcmp'; end
try set(Exp(expN).hOLb(i),'Visible','off')
catch
msg='No raw data RFcmp'
end
end
%Increment the CompositeTrace count and update the correlated reference OLAY cTraceIndx
Exp(expN).cTraceN= (Exp(expN).cTraceN) + 1 ;
Exp(expN).cTraceIndx(Exp(expN).cTraceN)= length(Exp(expN).hOL(:))+1;
%cPlotLB= strcat('Composite', num2str(cTraceN),'L=',num2str(Exp(expN).cLmean(cTraceN)),'Ls=',num2str(Exp(expN).cLstd(cTraceN))) %,'-',(Exp(expN).hOLname(cTraceIndx)))
%Exp(expN).cName(cTraceN)= {cPlotLB};
% Increment the CompositeTrace count and update the correlated reference OLAY cTraceIndx
Exp(expN).cTraceN=(Exp(expN).cTraceN) + 1 ;
Exp(expN).cTraceIndx(Exp(expN).cTraceN)=length(Exp(expN).hOL(:))+1;
%cPlotLB=strcat('Composite', num2str(cTraceN),'L=',num2str(Exp(expN).cLmean(cTraceN)),'Ls=',num2str(Exp(expN).cLstd(cTraceN))) %,'-',(Exp(expN).hOLname(cTraceIndx)))
%Exp(expN).cName(cTraceN)={cPlotLB};

493
workflow/apps/matlab/ezview/EZdestComp.m
View File

@@ -3,7 +3,7 @@
%Called by EZvDatatip.m and EZlstBoxExt.m
%Provides Trace data storage for use by EZfigTrendOL.m
if lstBoxCmpFlg== 1
if lstBoxCmpFlg==1
Exp(zoneSel).seltraceN=traceN;
seltraceN=traceN;
end
@@ -13,25 +13,23 @@ if expN==1 && get(ghandles.CompositeTog1,'value')==1 ||...
CompositeTrendFlg=1; else CompositeTrendFlg=0;
end
destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
if EZdatatip==1 %adaptation for image spot selection
%plNums= plateNum;
%destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
plNums= (MPsel-1)*destPerMP + (1:destPerMP)
% plNums=plateNum;
% destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
plNums=(MPsel-1)*destPerMP + (1:destPerMP)
zoneSel=expN;
tracN=Exp(zoneSel).traceN;
if zoneSel==1,Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1; end
if zoneSel==2,Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2; end
if zoneSel==3,Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3; end
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end
elseif EZdatatip==2 %adaption for Overlay plot selection
%destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
MPlateN= ceil(OLplateNum/destPerMP);
plNums= (MPlateN-1)*destPerMP + (1:destPerMP);
elseif EZdatatip==2 % adaption for Overlay plot selection
% destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
MPlateN=ceil(OLplateNum/destPerMP);
plNums=(MPlateN-1)*destPerMP + (1:destPerMP);
zoneSel=expN;
tracN=Exp(zoneSel).traceN;
if zoneSel==1,Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1; end
@@ -40,25 +38,22 @@ elseif EZdatatip==2 %adaption for Overlay plot selection
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end %2016_0222
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end %2016_0222
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end %2016_0222
elseif EZdatatip==0
if lstBoxCmpFlg~=1
DexpN= Exp(expN).DexpN;
plNums= (LBmp-1)*destPerMP + (1:destPerMP);
DexpN=Exp(expN).DexpN;
plNums=(LBmp-1)*destPerMP + (1:destPerMP);
tracN=Exp(zoneSel).traceN;
Exp(expN).Trace(traceN).DexpN= DexpN;
Exp(expN).Trace(traceN).DexpN=DexpN;
elseif lstBoxCmpFlg==1
DexpN= Exp(expN).DexpN;
DexpN=Exp(expN).DexpN;
tracN=Exp(zoneSel).traceN;
end
%determin if selection is a User chosen RF-****-mdG or RF-****-mdP
% determin if selection is a User chosen RF-****-mdG or RF-****-mdP
Lbl=cell2mat(selGnOrf);
if ~isempty(strfind(Lbl,'RF')) && ~isempty(strfind(Lbl,'md'))
strLoc= strfind(Lbl,'md');
MPloc= strfind(Lbl,':');
dMP= str2double(Lbl((MPloc(1)+1):(MPloc(2)-1)));
strLoc=strfind(Lbl,'md');
MPloc=strfind(Lbl,':');
dMP=str2double(Lbl((MPloc(1)+1):(MPloc(2)-1)));
if strcmp(Lbl(strLoc:strLoc+3),'-mdG(');
RFmdFlg='mdG';
elseif strcmp(Lbl(strLoc:strLoc+3),'-mdP(')
@@ -71,12 +66,11 @@ elseif EZdatatip==0
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end %2016_0222
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end %2016_0222
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end %2016_0222
end %if EZdatatip==1 %adaptation for image spot selection
end % if EZdatatip==1 %adaptation for image spot selection
if EZdatatip==2 %Response to Overlay click
%++++++++++++++++++++LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL+++++++++++++++++++++++
%seltraceN comes from EZvDatatip;
%Exp(OLay).seltraceN iscaptured from EZvDatatip
if EZdatatip==2 % Response to Overlay click
% seltraceN comes from EZvDatatip;
% Exp(OLay).seltraceN iscaptured from EZvDatatip
% if an OLay trace is selected
% else it is captured below if EZdatatip is not equal to 2
@@ -87,7 +81,7 @@ if EZdatatip==2 %Response to Overlay click
set(Exp(zoneSel).hL(seltraceN),'visible','on'); set(Exp(zoneSel).hLb(seltraceN),'visible','on');
catch, end
%Plot new intL
% Plot new intL
try
set(Exp(zoneSel).hintL(seltraceN),'visible','on'); set(Exp(zoneSel).hintLb(seltraceN),'visible','on');
catch, end
@@ -96,8 +90,7 @@ if EZdatatip==2 %Response to Overlay click
catch, end
if zoneSel==1,set(ghandles.DNLaxes1,'xlim',[-75,75]); end
%++++++++++++++++++++++KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK++++++++++++++++++++++
for J=1:(tracN),
for J=1:(tracN)
try
set(Exp(zoneSel).hKRF1(J),'visible','off'); set(Exp(zoneSel).hKRF2(J),'visible','off');
catch, end
@@ -111,7 +104,7 @@ if EZdatatip==2 %Response to Overlay click
try
set(Exp(zoneSel).hK(seltraceN),'visible','on'); set(Exp(zoneSel).hKb(seltraceN),'visible','on');
catch, end
%+++++++++++++++++++++rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr+++++++++++++++++++++++++++++
for J=1:(tracN),
try
set(Exp(zoneSel).hrRF1(J),'visible','off'); set(Exp(zoneSel).hrRF2(J),'visible','off');
@@ -126,13 +119,11 @@ if EZdatatip==2 %Response to Overlay click
try
set(Exp(zoneSel).hr(seltraceN),'visible','on'); set(Exp(zoneSel).hrb(seltraceN),'visible','on');
catch, end
else %if EZdatatip==1 or if EZdatatip==0 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%*************Plot RFmd1 and RFmd2 indexes*********************
if EZdatatip==0
end
%if ~exist(RFmdFlg)
else
% Plot RFmd1 and RFmd2 indexes
if EZdatatip==0
end
%if ~exist(RFmdFlg)
RF1mdIndx=Exp(zoneSel).Dexp(DexpN).RFmd1indx;
RF1mdPltN=Exp(zoneSel).Dexp(DexpN).RFmd1pltN;
RF2mdIndx=Exp(zoneSel).Dexp(DexpN).RFmd2indx;
@@ -140,70 +131,63 @@ end
try Rn=Exp(expN).Dexp(DexpN).RFmean; catch, Rn=0; end
try Rs=Exp(expN).Dexp(DexpN).RFstd; catch, Rs=0; end
if isempty(RF1mdIndx)
try Rn= Exp(expN).Dexp(DexpN).RFmeanG; catch, Rn=0; end
try Rs= Exp(expN).Dexp(DexpN).RFstdG; catch, Rs=0; end
end
try Rn=Exp(expN).Dexp(DexpN).RFmeanG; catch, Rn=0; end
try Rs=Exp(expN).Dexp(DexpN).RFstdG; catch, Rs=0; end
end
if lstBoxCmpFlg~= 1
Exp(zoneSel).seltraceN=tracN;
seltraceN=tracN;
end
%**************Plot L K r for all pertibation(destination) Plates***************
if lstBoxCmpFlg~= 1 % If selection is a "normal" item with a location in the label
try RF1mdNums= (RF1mdPltN-1)*destPerMP + (1:destPerMP); catch, end %RF1mdPltN %
try RF2mdNums= (RF2mdPltN-1)*destPerMP + (1:destPerMP); catch, end %RF2mdPltN %
if lstBoxCmpFlg~=1
Exp(zoneSel).seltraceN=tracN;
seltraceN=tracN;
end
% Plot L K r for all pertibation(destination) Plates
if lstBoxCmpFlg~=1 % If selection is a "normal" item with a location in the label
try RF1mdNums=(RF1mdPltN-1)*destPerMP + (1:destPerMP); catch, end %RF1mdPltN %
try RF2mdNums=(RF2mdPltN-1)*destPerMP + (1:destPerMP); catch, end %RF2mdPltN %
for I=1:length(plNums),
if CompositeTrendFlg==0 || EZdatatip==1 %'Normal' gene/orf spot image or listbox item with location data
Exp(expN).Trace(traceN).dmSel= pertSel;
Exp(expN).Trace(traceN).DexpN= DexpN;
Exp(expN).Trace(traceN).UsrGLB= selGnOrf; %usrGnSp;
Exp(expN).Trace(traceN).dmSel=pertSel;
Exp(expN).Trace(traceN).DexpN=DexpN;
Exp(expN).Trace(traceN).UsrGLB=selGnOrf; %usrGnSp;
if ~exist('RFmdFlg')
lvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,5);
if lvals(I)==0, lvals(I)=140; end
kvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,3);
rvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,4);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals= lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals= kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals= rvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals=lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals=kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals=rvals(I);
elseif strcmp(RFmdFlg,'mdG')
lvals(I)= Exp(expN).Dexp(DexpN).RFcmpGL.dm(I).med;
lvals(I)=Exp(expN).Dexp(DexpN).RFcmpGL.dm(I).med;
if lvals(I)==0, lvals(I)=140; end
kvals(I)= Exp(expN).Dexp(DexpN).RFcmpGK.dm(I).med;
rvals(I)= Exp(expN).Dexp(DexpN).RFcmpGr.dm(I).med;
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals= lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals= kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals= rvals(I);
kvals(I)=Exp(expN).Dexp(DexpN).RFcmpGK.dm(I).med;
rvals(I)=Exp(expN).Dexp(DexpN).RFcmpGr.dm(I).med;
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals=lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals=kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals=rvals(I);
elseif strcmp(RFmdFlg,'mdP')
lvals(I)= Exp(expN).Dexp(DexpN).RFmedianP(I,dMP);
lvals(I)=Exp(expN).Dexp(DexpN).RFmedianP(I,dMP);
if lvals(I)==0, lvals(I)=140; end
kvals(I)= scan(1,plNums(I)).plate(1).CFout(indx,3); %No P med.Kvals /dms currently avail.
rvals(I)= scan(1,plNums(I)).plate(1).CFout(indx,4); %No P med.rvals /dms currently avail.
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals= lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals= kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals= rvals(I);
kvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,3); %No P med.Kvals /dms currently avail.
rvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,4); %No P med.rvals /dms currently avail.
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals=lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals=kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals=rvals(I);
elseif strcmp(RFmdFlg,'md')
lvals(I)= Exp(expN).Dexp(DexpN).RFmean(I);
lvals(I)=Exp(expN).Dexp(DexpN).RFmean(I);
if lvals(I)==0, lvals(I)=140; end
kvals(I)= scan(1,plNums(I)).plate(1).CFout(indx,3); %No P med.Kvals /dms currently avail.
rvals(I)= scan(1,plNums(I)).plate(1).CFout(indx,4); %No P med.rvals /dms currently avail.
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals= lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals= kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals= rvals(I);
kvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,3); %No P med.Kvals /dms currently avail.
rvals(I)=scan(1,plNums(I)).plate(1).CFout(indx,4); %No P med.rvals /dms currently avail.
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals=lvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals=kvals(I);
Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals=rvals(I);
end
elseif CompositeTrendFlg==1 && EZdatatip==0 %Gene-Specifics Composite from listBox
lvals(I)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
if lvals(I)==0, lvals(I)=140; end
kvals(I)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals));
rvals(I)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals));
end %if CompositeTrendFlg==0 || EZdatatip==1
kvals(I)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrKvals));
rvals(I)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).Usrrvals));
end
try
if ~isempty(RF1mdIndx)
lvalsRF1md(I)=scan(1,RF1mdNums(I)).plate(1).CFout(RF1mdIndx(I),5);
@@ -211,14 +195,13 @@ if lstBoxCmpFlg~= 1 % If selection is a "normal" item with a location in the lab
kvalsRF1md(I)=scan(1,RF1mdNums(I)).plate(1).CFout(RF1mdIndx(I),3);
rvalsRF1md(I)=scan(1,RF1mdNums(I)).plate(1).CFout(RF1mdIndx(I),4);
elseif ~isempty(Exp(expN).Dexp(DexpN).RFcmpGL.dm(I).med)
lvalsRF1md(I)= Exp(expN).Dexp(DexpN).RFcmpGL.dm(I).med;
lvalsRF1md(I)=Exp(expN).Dexp(DexpN).RFcmpGL.dm(I).med;
if lvalsRF1md(I)==0, lvalsRF1md(I)=140; end
kvalsRF1md(I)= Exp(expN).Dexp(DexpN).RFcmpGK.dm(I).med;
rvalsRF1md(I)= Exp(expN).Dexp(DexpN).RFcmpGr.dm(I).med;
kvalsRF1md(I)=Exp(expN).Dexp(DexpN).RFcmpGK.dm(I).med;
rvalsRF1md(I)=Exp(expN).Dexp(DexpN).RFcmpGr.dm(I).med;
end
catch
end
try
lvalsRF2md(I)=scan(1,RF2mdNums(I)).plate(1).CFout(RF2mdIndx(I),5);
if lvalsRF2md(I)==0, lvalsRF2md(I)=140; end
@@ -226,198 +209,166 @@ if lstBoxCmpFlg~= 1 % If selection is a "normal" item with a location in the lab
rvalsRF2md(I)=scan(1,RF2mdNums(I)).plate(1).CFout(RF2mdIndx(I),4);
catch
end
%Added for INTERACTION Calculating Utility 2016_0219
% Added for INTERACTION Calculating Utility 2016_0219
try
if CompositeTrendFlg==0 || EZdatatip==1
Xn(I)=Exp(expN).Dexp(DexpN).scan(plNums(I)).plate(1).CFout(indx,5);
Xln(I)=Exp(expN).Dexp(DexpN).scan(plNums(I)).plate(1).CFout(indx,11);
Xhn(I)=Exp(expN).Dexp(DexpN).scan(plNums(I)).plate(1).CFout(indx,12);
elseif CompositeTrendFlg==1 && EZdatatip~=1
Xn(I)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
Xln(I)= Xn(I) - std(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
Xhn(I)= Xn(I) + std(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
Xn(I)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
Xln(I)=Xn(I) - std(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
Xhn(I)=Xn(I) + std(cell2mat(Exp(expN).Trace(tracN).Dexp(DexpN).DM(I).UsrLvals));
end
if Xn(I)==0, deltaXR(I)= 140; end
if Xn(I)==0, deltaXR(I)=140; end
if isnan(Xhn(I))||isnan(Xln(I))|| Xhn(I)==0||Xln(I)==0||isnan(Rs(I))
deltaXR(I)= 140;
elseif Xn(I) >= Rn(I)
deltaXR(I)= Xln(I)-(Rn(I)+Rs(I));
deltaXR(I)=140;
elseif Xn(I) >=Rn(I)
deltaXR(I)=Xln(I)-(Rn(I)+Rs(I));
else
deltaXR(I)= Xhn(I)-(Rn(I)-Rs(I));
deltaXR(I)=Xhn(I)-(Rn(I)-Rs(I));
end
catch
msg= 'No Refs! ->No Interaction Calculations!'
msg='No Refs! ->No Interaction Calculations!'
end
end %for I=1:length(plNums)
elseif lstBoxCmpFlg==1 %Determine values of RF1cmp or RFcmpG or RFcmpP composites
end
elseif lstBoxCmpFlg==1 %Determine values of RF1cmp or RFcmpG or RFcmpP composites
for dm=1:destPerMP
if RFcmpGFlg==0 %RF1cmp or RF2cmp clicked
lvals(dm)= Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(dm).med;
lvals(dm)=Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(dm).med;
if lvals(dm)==0, lvals(dm)=140; end
kvals(dm)= Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(dm).med;
rvals(dm)= Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(dm).med;
kvals(dm)=Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(dm).med;
rvals(dm)=Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(dm).med;
elseif RFcmpGFlg==1
lvals(dm)= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med;% Ls= num2str(l);
lvals(dm)=Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med;% Ls=num2str(l);
if lvals(dm)==0, lvals(dm)=140; end
kvals(dm)= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; %Ks= num2str(K);
rvals(dm)= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; %rs= num2str(r);
kvals(dm)=Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; %Ks=num2str(K);
rvals(dm)=Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; %rs=num2str(r);
end
%Added for INTERACTION Calculating Utility 2016_0219
% Added for INTERACTION Calculating Utility 2016_0219
try
Xn(dm)=lvals(dm);
Xln(dm)= lvals(dm)- Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std ;
Xhn(dm)= lvals(dm)+ Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
if Xn(dm)==0, deltaXR(dm)= 140; end
Xln(dm)=lvals(dm)- Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std ;
Xhn(dm)=lvals(dm)+ Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
if Xn(dm)==0, deltaXR(dm)=140; end
if isnan(Xhn(dm))||isnan(Xln(dm))|| Xhn(dm)==0||Xln(dm)==0||isnan(Rs(dm))
deltaXR(dm)= 140;
elseif Xn(dm) >= Rn(dm)
deltaXR(dm)= Xln(dm)-(Rn(dm)+Rs(dm));
deltaXR(dm)=140;
elseif Xn(dm) >=Rn(dm)
deltaXR(dm)=Xln(dm)-(Rn(dm)+Rs(dm));
else
deltaXR(dm)= Xhn(dm)-(Rn(dm)-Rs(dm));
deltaXR(dm)=Xhn(dm)-(Rn(dm)-Rs(dm));
end
catch
msg= 'No Refs! ->No Interaction Calculations!'
msg='No Refs! ->No Interaction Calculations!'
end
end % for dm=1:destPerMP
Exp(expN).Trace(traceN).UsrGLB=selGnOrf; %Added 18_0118 for tickLabelStr issue in EZfigTrendOL.m assoc'd with RFcmpG(-)
end
end %for dm=1:destPerMP
Exp(expN).Trace(traceN).UsrGLB= selGnOrf; %Added 18_0118 for tickLabelStr issue in EZfigTrendOL.m assoc'd with RFcmpG(-)
end %if lstBoxCmpFlg==1
%***********INTERACTION Plotting Utility 2016_0219*********************************************
try
if Rn(1)==0, % If Ref mean is zero
intL= 0; proGrIntL=0; intLadj=0; proGrIntLadj=0;
% INTERACTION Plotting Utility 2016_021
try
if Rn(1)==0 % if Ref mean is zero
intL=0; proGrIntL=0; intLadj=0; proGrIntLadj=0;
intNormL=6.66;intNormLadj=6.66; proGrIntNormL=6.66;proGrIntNormLadj=6.66;
else
%if Xn(I)==0 || Xn(I)==140,intL =140; else intL=(Xn-Rn); end
intL= (Xn-Rn);
intL(Xn==0)= 140;
intLadj=(deltaXR);
Exp(expN).Trace(tracN).Dexp(DexpN).UsrIntL= intL;
%{
intNormL=(intL) ./ Rn(1)
intNormLadj= ((deltaXR)./ Rn(1))
proGrIntL=-(intL)
proGrIntLadj=-(deltaXR)
proGrIntNormL=-(intL ./ Rn(1))
proGrIntNormLadj= -((deltaXR)./ Rn(1))
%find where Xn(j)==0 and set interactL to a fixed Max interaction value
intNormL(find(Xn==0))=2
intNormLadj(find(Xn==0))=2
proGrIntLadj(find(Xn==0))=-2
proGrIntNormLadj(find(Xn==0))=-2
%}
end
catch
FailMessage= 'Problem with Reference Rn value; Unable to produce Interaction values! Ln119 EZdestComp'
end
else
% if Xn(I)==0 || Xn(I)==140,intL =140; else intL=(Xn-Rn); end
intL=(Xn-Rn);
intL(Xn==0)=140;
intLadj=(deltaXR);
Exp(expN).Trace(tracN).Dexp(DexpN).UsrIntL=intL;
%{
intNormL=(intL) ./ Rn(1)
intNormLadj=((deltaXR)./ Rn(1))
proGrIntL=-(intL)
proGrIntLadj=-(deltaXR)
proGrIntNormL=-(intL ./ Rn(1))
proGrIntNormLadj=-((deltaXR)./ Rn(1))
%find where Xn(j)==0 and set interactL to a fixed Max interaction value
intNormL(find(Xn==0))=2
intNormLadj(find(Xn==0))=2
proGrIntLadj(find(Xn==0))=-2
proGrIntNormLadj(find(Xn==0))=-2
%}
end
catch
FailMessage='Problem with Reference Rn value; Unable to produce Interaction values! Ln119 EZdestComp'
end
hidem(ghandles.Daxes1)
if zoneSel==1,showm(ghandles.Dlaxes1);showm(ghandles.Dkaxes1);showm(ghandles.Draxes1);end
if zoneSel==2,showm(ghandles.Dlaxes2);showm(ghandles.Dkaxes2);showm(ghandles.Draxes2);end
if zoneSel==3,showm(ghandles.Dlaxes3);showm(ghandles.Dkaxes3);showm(ghandles.Draxes3);end
set(Dlaxes,'NextPlot','add'); set(Dkaxes,'NextPlot','add'); set(Draxes,'NextPlot','add')
if zoneSel==1,showm(ghandles.DNLaxes1); end
if zoneSel==2,showm(ghandles.DNLaxes2); end
if zoneSel==3,showm(ghandles.DNLaxes3); end
set(DNLaxes,'NextPlot','add');
%+++++++++++++++++LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL+++++++++++++++++++++++++++++++++
%Make visible the current L plot and store it for retrieval by OLay code
% Make visible the current L plot and store it for retrieval by OLay code
if verLessThan('matlab','8.4')
else %accomodate new matlab changes after 2014a fix 23_0807
tempFig2= figure;
else % accomodate new matlab changes after 2014a fix 23_0807
tempFig2=figure;
end
try %Some experiments do not have ref. plates
Exp(zoneSel).hLRF1(tracN)= plot(Dlaxes,lvalsRF1md,1:destPerMP,'b'); hold on
try % some experiments do not have ref. plates
Exp(zoneSel).hLRF1(tracN)=plot(Dlaxes,lvalsRF1md,1:destPerMP,'b'); hold on
catch
end
try
Exp(zoneSel).hLRF2(tracN)= plot(Dlaxes,lvalsRF2md,1:destPerMP,'c'); hold on
Exp(zoneSel).hLRF2(tracN)=plot(Dlaxes,lvalsRF2md,1:destPerMP,'c'); hold on
catch
end
try
Exp(zoneSel).hL(tracN)= plot(Dlaxes,lvals,1:destPerMP); Exp(zoneSel).hLb(tracN)= plot(Dlaxes,lvals,1:destPerMP,'rs');
Exp(zoneSel).hL(tracN)=plot(Dlaxes,lvals,1:destPerMP); Exp(zoneSel).hLb(tracN)=plot(Dlaxes,lvals,1:destPerMP,'rs');
catch
end
if zoneSel==1,set(ghandles.Dlaxes1,'xlim',[0,140]); end
if zoneSel==2,set(ghandles.Dlaxes2,'xlim',[0,140]); end
if zoneSel==3,set(ghandles.Dlaxes3,'xlim',[0,140]); end
%*************************************************
%Make visible Plot for Interaction Data, Store and Hide unless a N (InteractionPBsel) set that plot on Top of the RawData Plots.
%Plot new intL
% Make visible Plot for Interaction Data, Store and Hide unless a N (InteractionPBsel) set that plot on Top of the RawData Plots.
% Plot new intL
try
% zeroCLn= zeros(1,destPerMP)
% zeroCLn=zeros(1,destPerMP)
% Exp(zoneSel).hzeroCLn=plot(DNLaxes,zeroCLn,1:destPerMP,'y');
Exp(zoneSel).hintL(tracN)= plot(DNLaxes,intL,1:destPerMP); Exp(zoneSel).hintLb(tracN)= plot(DNLaxes,intL,1:destPerMP,'rs');
Exp(zoneSel).hintLadj(tracN)= plot(DNLaxes,intLadj,1:destPerMP,'g'); Exp(zoneSel).hintLadjb(tracN)= plot(DNLaxes,intLadj,1:destPerMP,'gs');
catch,
Exp(zoneSel).hintL(tracN)=plot(DNLaxes,intL,1:destPerMP); Exp(zoneSel).hintLb(tracN)=plot(DNLaxes,intL,1:destPerMP,'rs');
Exp(zoneSel).hintLadj(tracN)=plot(DNLaxes,intLadj,1:destPerMP,'g'); Exp(zoneSel).hintLadjb(tracN)=plot(DNLaxes,intLadj,1:destPerMP,'gs');
catch
end
if zoneSel==1,set(ghandles.DNLaxes1,'xlim',[-75,75]); end
if zoneSel==2,set(ghandles.DNLaxes2,'xlim',[-75,75]); end
if zoneSel==3,set(ghandles.DNLaxes3,'xlim',[-75,75]); end
%intNormL
%intNormLadj
%********************************************
%ProGrIntLadj Plot
%ProGrintLadj Plot
%ProGrintNormL
%proGrintNormLadj
%+++++++++++++++++KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK+++++++++++++++++++++++++++++++++++++++++++++++++++++++
%Hide all K plots
% intNormL
% intNormLadj
% ProGrIntLadj Plot
% ProGrintLadj Plot
% ProGrintNormL
% proGrintNormLadj
% Hide all K plots
for J=1:(tracN-1),
try
set(Exp(zoneSel).hKRF1(J),'visible','off'); set(Exp(zoneSel).hKRF2(J),'visible','off');
catch, end
catch
end
try
set(Exp(zoneSel).hK(J),'visible','off'); set(Exp(zoneSel).hKb(J),'visible','off');
catch, end
catch
end
end
%Make visible the current L plot and store it for retrieval by OLay code
try %Some experiments do not have ref. plates
Exp(zoneSel).hKRF1(tracN)= plot(Dkaxes,kvalsRF1md,1:destPerMP,'b');
Exp(zoneSel).hKRF2(tracN)= plot(Dkaxes,kvalsRF2md,1:destPerMP,'c');
catch, end
try
Exp(zoneSel).hK(tracN)= plot(Dkaxes,kvals,1:destPerMP,'b'); Exp(zoneSel).hKb(tracN)= plot(Dkaxes,kvals,1:destPerMP,'rs');
catch, end
set(Dkaxes,'xlim',[0,200]) %max(kvals+20)
set(Dkaxes,'ycolor',[.9,.9,1])
%++++++++++++++++++rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr+++++++++++++++++++++++++++++++++++++++++++++++
%Hide all r plots
% Make visible the current L plot and store it for retrieval by OLay code
try % some experiments do not have ref. plates
Exp(zoneSel).hKRF1(tracN)=plot(Dkaxes,kvalsRF1md,1:destPerMP,'b');
Exp(zoneSel).hKRF2(tracN)=plot(Dkaxes,kvalsRF2md,1:destPerMP,'c');
catch
end
try
Exp(zoneSel).hK(tracN)=plot(Dkaxes,kvals,1:destPerMP,'b'); Exp(zoneSel).hKb(tracN)=plot(Dkaxes,kvals,1:destPerMP,'rs');
catch
end
set(Dkaxes,'xlim',[0,200]) % max(kvals+20)
set(Dkaxes,'ycolor',[.9,.9,1])
% Hide all r plots
for J=1:(tracN-1),
try
set(Exp(zoneSel).hrRF1(J),'visible','off'); set(Exp(zoneSel).hrRF2(J),'visible','off');
@@ -426,34 +377,25 @@ end
set(Exp(zoneSel).hr(J),'visible','off'); set(Exp(zoneSel).hrb(J),'visible','off');
catch, end
end
%Make visible the current r plot and store it for retrieval by OLay code
% Make visible the current r plot and store it for retrieval by OLay code
try %Some experiments do not have ref. plates
Exp(zoneSel).hrRF1(tracN)= plot(Draxes,rvalsRF1md,1:destPerMP,'b');
Exp(zoneSel).hrRF2(tracN)= plot(Draxes,rvalsRF2md,1:destPerMP,'c');
Exp(zoneSel).hrRF1(tracN)=plot(Draxes,rvalsRF1md,1:destPerMP,'b');
Exp(zoneSel).hrRF2(tracN)=plot(Draxes,rvalsRF2md,1:destPerMP,'c');
catch, end
try
Exp(zoneSel).hr(tracN)= plot(Draxes,rvals,1:destPerMP,'b'); Exp(zoneSel).hrb(tracN)= plot(Draxes,rvals,1:destPerMP,'rs');
Exp(zoneSel).hr(tracN)=plot(Draxes,rvals,1:destPerMP,'b'); Exp(zoneSel).hrb(tracN)=plot(Draxes,rvals,1:destPerMP,'rs');
catch, end
set(Draxes,'xlim',[0,1])
set(Draxes,'ycolor',[.9,.9,1])
end
if zoneSel==1, set(ghandles.geneOrfLKr1,'string', grfgenestr);end
if zoneSel==2, set(ghandles.geneOrfLKr2,'string', grfgenestr);end
if zoneSel==3, set(ghandles.geneOrfLKr3,'string', grfgenestr);end
end %if EZdatatip==2 Response to Overlay click
if zoneSel==1, set(ghandles.geneOrfLKr1,'string', grfgenestr);end
if zoneSel==2, set(ghandles.geneOrfLKr2,'string', grfgenestr);end
if zoneSel==3, set(ghandles.geneOrfLKr3,'string', grfgenestr);end
%*********************************************************************************************************************
%*********************************************************************************************************************
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%___________________________________Display Selection PlotFilter ____________________
if Exp(4).interacPBsel==0 %00000000000000000000000000000
% Display Selection PlotFilter
if Exp(4).interacPBsel==0
% replace ghandles.DNLaxes1 (Dlaxes2)etc. with a single
% Exp(zoneSel).DNLaxes,....
set(ghandles.Dlaxes1,'Visible','on')
@@ -470,7 +412,6 @@ end %if EZdatatip==2 Response to Overlay click
try
set(Exp(zoneSel).hL(n),'visible','off'); set(Exp(zoneSel).hLb(n),'visible','off');
catch, end
try
set(Exp(zoneSel).hintL(n),'visible','off'); set(Exp(zoneSel).hintLb(n),'visible','off');
catch, end
@@ -488,10 +429,7 @@ end %if EZdatatip==2 Response to Overlay click
for i=1:Exp(zoneSel).expLoadCnt,
try set(Exp(zoneSel).hzeroCLn(i),'visible','off'); catch ME, end
end
elseif Exp(4).interacPBsel==1 %111111111111111111111111111
elseif Exp(4).interacPBsel==1
set(ghandles.DNLaxes1,'Visible','on')
set(ghandles.DNLaxes2,'Visible','on')
set(ghandles.DNLaxes3,'Visible','on')
@@ -512,47 +450,18 @@ end %if EZdatatip==2 Response to Overlay click
for i=1:Exp(zoneSel).expLoadCnt,
try set(Exp(zoneSel).hzeroCLn(i),'visible','on'); catch ME, end
end
elseif Exp(4).interacPBsel==2 %2222222222222222222222222222 TEMPorily Same as interacPBsel==1
% set(ghandles.DNLaxes1,'Visible','on')
%set(ghandles.Dlaxes1,'Visible','off')
elseif Exp(4).interacPBsel==2
end
end %if Exp(4).interacPBsel==0
if verLessThan('matlab','8.4')
else %accomodate new matlab changes after 2014a fix update 23_0807
if verLessThan('matlab','8.4')
else % accomodate new matlab changes after 2014a fix update 23_0807
close(tempFig2)
end
%------------------------------------------------------------------------------------------------------------
end
%=====================================================================================================================
% Deprecated functions
%end %if isempty(msg)
%BONEYARD BONEYARD BONEYARD BONEYARD BONEYARD BONEYARD BONEYARD BONEYARD BONEYARD
%*********************************************************************************
%{
%{
for J=1:(tracN),
try
set(Exp(zoneSel).hintL(J),'visible','off'); set(Exp(zoneSel).hintLb(J),'visible','off');
@@ -562,7 +471,7 @@ end %if EZdatatip==2 Response to Overlay click
catch, end
end
%}
%{
%{
for J=1:(tracN),
try
set(Exp(zoneSel).hLRF1(J),'visible','off'); set(Exp(zoneSel).hLRF2(J),'visible','off');
@@ -574,7 +483,7 @@ end %if EZdatatip==2 Response to Overlay click
%}
%Hide all L plots
%{
%{
for J=1:(tracN-1),
try
set(Exp(zoneSel).hLRF1(J),'visible','off'); set(Exp(zoneSel).hLRF2(J),'visible','off');
@@ -583,26 +492,26 @@ end %if EZdatatip==2 Response to Overlay click
set(Exp(zoneSel).hL(J),'visible','off'); set(Exp(zoneSel).hLb(J),'visible','off');
catch, end
end
%}
%Hide all intL plots
%{
for J=1:(tracN),
%}
%Hide all intL plots
%{
for J=1:(tracN),
try
set(Exp(zoneSel).hintL(J),'visible','off'); set(Exp(zoneSel).hintLb(J),'visible','off');
catch, end
try
set(Exp(zoneSel).hintLadj(J),'visible','off'); set(Exp(zoneSel).hintLadjb(J),'visible','off');
catch, end
end
%}
end
%}
% set(Dlaxes,'xlim',[0,max(lvals+20)])
% catch
% set(Dlaxes,'xlim',[0,max(lvals+20)])
% catch
% set(Dlaxes,'NextPlot','add');
% Exp(zoneSel).hL(tracN)= plot(Dlaxes,lvals,1:destPerMP);
% Exp(zoneSel).hLb(tracN)= plot(Dlaxes,lvals,1:destPerMP,'rs');
% Exp(zoneSel).hL(tracN)=plot(Dlaxes,lvals,1:destPerMP);
% Exp(zoneSel).hLb(tracN)=plot(Dlaxes,lvals,1:destPerMP,'rs');
%hDaxL=plot(Dlaxes,lvals,1:destPerMP);hold(Dlaxes); plot(Dlaxes,lvals,1:destPerMP,'rs');...
% hold(Dlaxes);
@@ -618,14 +527,14 @@ end %if EZdatatip==2 Response to Overlay click
%{
try
hDaxK= plot(Dkaxes,kvalsRF1md,1:destPerMP,'y'); hold(Dkaxes); plot(Dkaxes,kvalsRF2md,1:destPerMP,'y');...
hDaxK=plot(Dkaxes,kvalsRF1md,1:destPerMP,'y'); hold(Dkaxes); plot(Dkaxes,kvalsRF2md,1:destPerMP,'y');...
plot(Dkaxes,kvals,1:destPerMP); plot(Dkaxes,kvals,1:destPerMP,'rs');...
hold(Dkaxes);
set(Dkaxes,'xlim',[0,200]) %max(kvals+20)
set(Dkaxes,'ycolor',[.9,.9,1])
catch
set(Dkaxes,'NextPlot','replace');
hDaxK= plot(Dkaxes,kvals,1:destPerMP); hold(Dkaxes); plot(Dkaxes,kvals,1:destPerMP,'rs');...
hDaxK=plot(Dkaxes,kvals,1:destPerMP); hold(Dkaxes); plot(Dkaxes,kvals,1:destPerMP,'rs');...
hold(Dkaxes);
set(Dkaxes,'xlim',[0,200]) %max(kvals+20)
set(Dkaxes,'ycolor',[.9,.9,1])
@@ -634,16 +543,16 @@ end %if EZdatatip==2 Response to Overlay click
%{
try
hDaxR= plot(Draxes,rvalsRF1md,1:destPerMP,'y'); hold(Draxes); plot(Draxes,rvalsRF2md,1:destPerMP,'y');...
hDaxR=plot(Draxes,rvalsRF1md,1:destPerMP,'y'); hold(Draxes); plot(Draxes,rvalsRF2md,1:destPerMP,'y');...
plot(Draxes,rvals,1:destPerMP); plot(Draxes,rvals,1:destPerMP,'rs');...
hold(Draxes);
set(Draxes,'xlim',[0,1])
set(Draxes,'ycolor',[.9,.9,1])
catch
set(Draxes,'NextPlot','replace')
hDaxR= plot(Draxes,rvals,1:destPerMP); hold(Draxes); plot(Draxes,rvals,1:destPerMP,'rs');...
hDaxR=plot(Draxes,rvals,1:destPerMP); hold(Draxes); plot(Draxes,rvals,1:destPerMP,'rs');...
hold(Draxes);
set(Draxes,'xlim',[0,1])
set(Draxes,'ycolor',[.9,.9,1])
end
%}
%}

2
workflow/apps/matlab/ezview/EZdiagRFsSheet.m
View File

@@ -1,5 +1,5 @@
global Exp
try %Try the whole routine
try % Try the whole routine
if strcmp(Exp(expN).DexpType,'multi') ||...
strcmp(Exp(expN).DexpType,'chrono')

38
workflow/apps/matlab/ezview/EZdiagRFsSheetwImport.m
View File

@@ -1,4 +1,4 @@
%Diagnostic sheet called by EZvInitLoad.m, EZexpSel.m ?EZinteractDev_.m?
% Diagnostic sheet called by EZvInitLoad.m, EZexpSel.m ?EZinteractDev_.m?
global Exp
intLfilename1=fullfile(Exp(expN).resDir,'PrintResults','!RFsDiagnostics.txt');
@@ -7,8 +7,8 @@ ln=1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'%s\ExpName:::','Reference Diagnostic Values');
%will need to reverse the equals pulling data from the Exp source as needed
%to populate the printout diagnostice sheet.
% Will need to reverse the equals pulling data from the Exp source as needed
% to populate the printout diagnostice sheet.
for d=1:DMnum
fprintf(fid,'RF Name\Median\Mean\STD\Max\Min');
fprintf(fid,'\n')
@@ -36,40 +36,28 @@ for d=1:DMnum
RFmeanG=Exp(expN).minG(d,dMPs(mm));
maxG= Exp(expN).maxG(d,dMPs(mm));
minG= Exp(expN).minG(d,dMPs(mm));
end %for d=1:DMnum
end
for mm=1:length(dMPs)
for d=1:DMnum
RFmd1posD= Exp(expN).RFmdPindx(d,dMPs(mm));
dMP= Exp(expN).RFmdPpltN(d,dMPs(mm)); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
dMP= Exp(expN).RFmdPpltN(d,dMPs(mm)); % This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
rf1scNdisp= Exp(expN).RFmdPscanN(d,dMPs(mm));
mval1Disp= Exp(expN).RFmedianP(d,dMPs(mm));
std1Disp= Exp(expN).stdP(d,dMPs(mm));
mean1Disp= Exp(expN).meanP(d,dMPs(mm));
minDisp= Exp(expN).minP(d,dMPs(mm));
maxDisp= Exp(expN).maxP(d,dMPs(mm));
end %for d=1:DMnum
end %for mm=1:length(dMPs)
end
end
%{
RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
rf12mean(RFcombValList)= Exp(expN).RFmean(d+1);
std12(RFcombValList)= Exp(expN).RFstd(d+1);
Exp(expN).RFmin(d+1)=min(RFcombValList);
Exp(expN).RFmax(d+1)=max(RFcombValList);
%}
RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
rf12mean(RFcombValList)= Exp(expN).RFmean(d+1);
std12(RFcombValList)= Exp(expN).RFstd(d+1);
Exp(expN).RFmin(d+1)=min(RFcombValList);
Exp(expN).RFmax(d+1)=max(RFcombValList);
%}
fclose(fid)

1514
workflow/apps/matlab/ezview/EZexpSel.m
View File

File diff suppressed because it is too large Load Diff

663
workflow/apps/matlab/ezview/EZfigTrendOL.m
View File

@@ -2,14 +2,13 @@
%Uses data stored from OLay ; Clearing OLay clears data used by this
%Trending Utility
global Exp
global userPars
%try
kfiltLim= userPars.kfiltLim;
kfiltLim=userPars.kfiltLim;
%catch
%kfiltLim= str2double(userPars.BPdefault(6));
%kfiltLim=str2double(userPars.BPdefault(6));
%end
if get(handles.CompositeTog1, 'Value')
@@ -18,220 +17,206 @@ else
cmpTogFlg=0;
end
DexpN= Exp(expN).DexpN;
if strcmp(Exp(expN).DexpType, 'chrono')
maxRows=1; Lmax= 1; bpInd=0;
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
dmSel= Exp(expN).Trace(trc).dmSel;
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
rows= length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
rows=1;
end
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
if rows> maxRows, maxRows= rows; end
LsmpMax= max(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
LsmpMax= max(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
end
if LsmpMax> Lmax, Lmax= LsmpMax; end
bpInd=bpInd+1;
end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
catch
end
end % for trc= 1:
end %for n=1:length(Exp(expN).Dexp)
maxCols= bpInd; %length(Exp(expN).Dexp) * length(Exp(expN).Trace)
BPvals(1:maxRows,1:maxCols)= nan; %BoxPlot requires a matrix with uniform length even if data is not of the same length
bpInd=0;
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
dmSel= Exp(expN).Trace(trc).dmSel;
bpInd=bpInd+1;
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
kFiltrIndx= find((cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<= kfiltLim);
tmp= cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
BPvals(1:length(kFiltrIndx),bpInd)= tmp(kFiltrIndx);
%BPvals(1:length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)),bpInd)= cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
cnt= length(kFiltrIndx); %length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
if length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)> 1 %>= 1
kFiltrIndx= find(((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<= kfiltLim);
tmp= Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
BPvals(1:length(kFiltrIndx),bpInd)= tmp(kFiltrIndx);
cnt= length(kFiltrIndx);
%BPvals(1:length((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)),bpInd)= Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
%cnt= length((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
BPvals(1,bpInd)= Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
cnt= length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
end
end
%scnt(bpInd)= strcat('[',num2str(cnt),']');
scnt= strcat('[',num2str(cnt),']');
%Get Agar DrugMedia
drug= Exp(expN).Dexp(n).DM.drug{dmSel};
conc= Exp(expN).Dexp(n).DM.conc{dmSel};
media= Exp(expN).Dexp(n).DM.media{dmSel};
mod1= Exp(expN).Dexp(n).DM.mod1{dmSel}; if isnan(cell2mat(mod1)), mod1='';end
conc1= Exp(expN).Dexp(n).DM.conc1{dmSel}; if isnan(cell2mat(conc1)), conc1='';end
mod2= Exp(expN).Dexp(n).DM.mod2{dmSel}; if isnan(cell2mat(mod2)), mod2='';end
conc2=Exp(expN).Dexp(n).DM.conc2{dmSel}; if isnan(cell2mat(conc2)), conc2='';end
dmStr= strcat(drug,conc,'_',media,'_',mod1,conc1,mod2,conc2);
%Extract expDay from ExpName string
dayNpos= max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'));
dayLbl= Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);
label= strcat(dayLbl,'-', Exp(expN).Trace(trc).UsrGLB, dmStr,scnt); %scnt(bpInd));
tickLabelStr{bpInd}= label;
end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
catch
end
end %for trc=
end %for n=1:length(Exp(expN).Dexp)
else %if 'single' or 'multi' experiment setup for DM trends
maxRows=1; Lmax= 1; bpInd=0;
%for n=1:length(Exp(expN).Dexp) %LOOP Thru Multi Experiments
DexpN=Exp(expN).DexpN;
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru DM perturbations
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
% tempLB= Exp(expN).Trace(trc).UsrGLB;
if strcmp(Exp(expN).DexpType, 'chrono')
maxRows=1; Lmax=1; bpInd=0;
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
dmSel=Exp(expN).Trace(trc).dmSel;
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
rows=length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
rows=1;
end
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
if rows> maxRows, maxRows=rows; end
LsmpMax=max(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
LsmpMax=max(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
end
if LsmpMax> Lmax, Lmax=LsmpMax; end
bpInd=bpInd+1;
end % if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
catch
end
end
end
maxCols=bpInd; % length(Exp(expN).Dexp) * length(Exp(expN).Trace)
BPvals(1:maxRows,1:maxCols)=nan; % BoxPlot requires a matrix with uniform length even if data is not of the same length
bpInd=0;
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
dmSel=Exp(expN).Trace(trc).dmSel;
bpInd=bpInd+1;
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
kFiltrIndx=find((cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<=kfiltLim);
tmp=cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
BPvals(1:length(kFiltrIndx),bpInd)=tmp(kFiltrIndx);
% BPvals(1:length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)),bpInd)=cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
cnt=length(kFiltrIndx); %length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
if length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)> 1 %>=1
kFiltrIndx=find(((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<=kfiltLim);
tmp=Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
BPvals(1:length(kFiltrIndx),bpInd)=tmp(kFiltrIndx);
cnt=length(kFiltrIndx);
% BPvals(1:length((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)),bpInd)=Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
% cnt=length((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
BPvals(1,bpInd)=Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals;
cnt=length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
end
end
DexpN= Exp(expN).Trace(trc).DexpN;
% scnt(bpInd)=strcat('[',num2str(cnt),']');
scnt=strcat('[',num2str(cnt),']');
% Get Agar DrugMedia
drug=Exp(expN).Dexp(n).DM.drug{dmSel};
conc=Exp(expN).Dexp(n).DM.conc{dmSel};
media=Exp(expN).Dexp(n).DM.media{dmSel};
mod1=Exp(expN).Dexp(n).DM.mod1{dmSel}; if isnan(cell2mat(mod1)), mod1='';end
conc1=Exp(expN).Dexp(n).DM.conc1{dmSel}; if isnan(cell2mat(conc1)), conc1='';end
mod2=Exp(expN).Dexp(n).DM.mod2{dmSel}; if isnan(cell2mat(mod2)), mod2='';end
conc2=Exp(expN).Dexp(n).DM.conc2{dmSel}; if isnan(cell2mat(conc2)), conc2='';end
dmStr=strcat(drug,conc,'_',media,'_',mod1,conc1,mod2,conc2);
% Extract expDay from ExpName string
dayNpos=max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'));
dayLbl=Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);
label=strcat(dayLbl,'-', Exp(expN).Trace(trc).UsrGLB, dmStr,scnt); %scnt(bpInd));
tickLabelStr{bpInd}=label;
end
catch
end
end
end
else % if 'single' or 'multi' experiment setup for DM trends
maxRows=1; Lmax=1; bpInd=0;
% for n=1:length(Exp(expN).Dexp) % Loop Thru Multi Experiments
DexpN=Exp(expN).DexpN;
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug) % LOOP Thru DM perturbations
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
% tempLB=Exp(expN).Trace(trc).UsrGLB;
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
DexpN=Exp(expN).Trace(trc).DexpN;
if iscell(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)
rows= length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
rows=length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
else
rows=1;
end
if iscell(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)
if rows> maxRows, maxRows= rows; end
LsmpMax= max(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
if rows> maxRows, maxRows=rows; end
LsmpMax=max(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
else
LsmpMax= max(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
LsmpMax=max(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
end
if LsmpMax> Lmax, Lmax= LsmpMax; end
if LsmpMax> Lmax, Lmax=LsmpMax; end
bpInd=bpInd+1;
end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
end
catch
end
end % for trc= 1:
end %for
%end %for n=1:length(Exp(expN).Dexp)
%end
maxCols= bpInd; %length(Exp(expN).Dexp) * length(Exp(expN).Trace)
BPvals(1:maxRows,1:maxCols)= nan; %BoxPlot requires a matrix with uniform length even if data is not of the same length
bpInd=0;
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru DM perturbations
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
end
end
% end <- to stop here
maxCols=bpInd; % length(Exp(expN).Dexp) * length(Exp(expN).Trace)
BPvals(1:maxRows,1:maxCols)=nan; % BoxPlot requires a matrix with uniform length even if data is not of the same length
bpInd=0;
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru DM perturbations
for trc=1:Exp(expN).traceN % length(Exp(expN).Trace)
try
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
DexpN= Exp(expN).Trace(trc).DexpN;
DexpN=Exp(expN).Trace(trc).DexpN;
bpInd=bpInd+1;
if iscell(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)
kFiltrIndx= find((cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrKvals))<= kfiltLim);
tmp= cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
BPvals(1:length(kFiltrIndx),bpInd)= tmp(kFiltrIndx);
cnt= length(kFiltrIndx);
%BPvals(1:length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)),bpInd)= cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
%cnt= length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
kFiltrIndx=find((cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrKvals))<=kfiltLim);
tmp=cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
BPvals(1:length(kFiltrIndx),bpInd)=tmp(kFiltrIndx);
cnt=length(kFiltrIndx);
%BPvals(1:length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)),bpInd)=cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
%cnt=length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals));
else
if length(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals)> 1
kFiltrIndx= find(((Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrKvals))<= kfiltLim);
tmp= Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals;
BPvals(1:length(kFiltrIndx),bpInd)= tmp(kFiltrIndx);
cnt= length(kFiltrIndx);
kFiltrIndx=find(((Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrKvals))<=kfiltLim);
tmp=Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals;
BPvals(1:length(kFiltrIndx),bpInd)=tmp(kFiltrIndx);
cnt=length(kFiltrIndx);
else
BPvals(1,bpInd)= Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals;
cnt= length(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
BPvals(1,bpInd)=Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals;
cnt=length(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
end
end
%scnt(bpInd)= {strcat('[',num2str(cnt),']')};
scnt= {strcat('[',num2str(cnt),']')};
%Get Agar DrugMedia
drug= Exp(expN).Dexp(DexpN).DM.drug{dm};
conc= Exp(expN).Dexp(DexpN).DM.conc{dm};
media= Exp(expN).Dexp(DexpN).DM.media{dm};
mod1= Exp(expN).Dexp(DexpN).DM.mod1{dm}; if isnan(cell2mat(mod1)), mod1='';end
conc1= Exp(expN).Dexp(DexpN).DM.conc1{dm}; if isnan(cell2mat(conc1)), conc1='';end
mod2= Exp(expN).Dexp(DexpN).DM.mod2{dm}; if isnan(cell2mat(mod2)), mod2='';end
% scnt(bpInd)={strcat('[',num2str(cnt),']')};
scnt={strcat('[',num2str(cnt),']')};
% Get Agar DrugMedia
drug=Exp(expN).Dexp(DexpN).DM.drug{dm};
conc=Exp(expN).Dexp(DexpN).DM.conc{dm};
media=Exp(expN).Dexp(DexpN).DM.media{dm};
mod1=Exp(expN).Dexp(DexpN).DM.mod1{dm}; if isnan(cell2mat(mod1)), mod1='';end
conc1=Exp(expN).Dexp(DexpN).DM.conc1{dm}; if isnan(cell2mat(conc1)), conc1='';end
mod2=Exp(expN).Dexp(DexpN).DM.mod2{dm}; if isnan(cell2mat(mod2)), mod2='';end
conc2=Exp(expN).Dexp(DexpN).DM.conc2{dm}; if isnan(cell2mat(conc2)), conc2='';end
dmStr= strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
dmStr=strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
%Extract expDay from ExpName string
dayNpos= max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
dayLbl= Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
% Extract expDay from ExpName string
dayNpos=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
dayLbl=Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
if ~isempty(dayLbl), dayLbl=strcat(dayLbl,'_'); end
label= strcat(dayLbl,Exp(expN).Trace(trc).UsrGLB, dmStr,scnt);
tickLabelStr{bpInd}= label;
label=strcat(dayLbl,Exp(expN).Trace(trc).UsrGLB, dmStr,scnt);
tickLabelStr{bpInd}=label;
end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
catch
end
end %for trc=
end %for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug)
%{
end
end
%{
if isequal(tempLB(4:6),'cmp')||isequal(tempLB(3:6),'cmpG'),
RFcmpFlg=1;
else
RFcmpFlg=0;
end
%}
%}
end
end %if strcmp(Exp(expN).DexpType, 'chrono') else if Single or Multi experiment
%***********************************************************************************************
%Box Plot Plotting section
% Box Plot Plotting section
if userPars.boxplotFlg==1
BPoutliers= userPars.BPoutliers;
BPnotch= userPars.BPnotch;
sh= userPars.BPlblShft;
fontSize= userPars.BPfontSz;
rotation= userPars.BProt;
BPoutliers=userPars.BPoutliers;
BPnotch=userPars.BPnotch;
sh=userPars.BPlblShft;
fontSize=userPars.BPfontSz;
rotation=userPars.BProt;
%fontSize=8;
%tickLabelStr={'Label alpha','Label beta','Label chi','Label delta',...
% 'Label epsilon','Label fish','Label gamma','Label hallo','Label ingo'}
% fontSize=8;
% tickLabelStr={'Label alpha','Label beta','Label chi','Label delta',...
%'Label epsilon','Label fish','Label gamma','Label hallo','Label ingo'}
% generate data
if size(BPvals,1)==1, BPvals(2,1:maxCols)= nan; end
if size(BPvals,1)==1, BPvals(2,1:maxCols)=nan; end
final_res=BPvals; %10*randn(300,9)+10;
% group boxes
%sh=0.3; %sh is shift value
% sh=0.3; %sh is shift value
width=.5*sh;
%pos=[1+sh 2-sh 3+sh 4-sh 5+sh 6-sh 7+sh 8-sh 9+sh];
% pos=[1+sh 2-sh 3+sh 4-sh 5+sh 6-sh 7+sh 8-sh 9+sh];
bpn=1;
if strcmp(Exp(expN).DexpType, 'chrono')
ticDim= length(Exp(expN).Dexp);
ticDim=length(Exp(expN).Dexp);
else
ticDim= length(Exp(expN).Dexp(DexpN).DM.drug);
ticDim=length(Exp(expN).Dexp(DexpN).DM.drug);
end
for dim=1:ticDim %LOOP Thru DM perturbations
for dim=1:ticDim % LOOP Thru DM perturbations
shn=0;
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
for trc=1:Exp(expN).traceN % length(Exp(expN).Trace)
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
pos(bpn)= dim + (shn*sh);
shn= shn+1;
bpn= bpn+1;
pos(bpn)=dim + (shn*sh);
shn=shn+1;
bpn=bpn+1;
end
end
end
@@ -240,12 +225,14 @@ rotation= userPars.BProt;
% boxplot
figure
set(gcf,'OuterPosition',(get(0,'screensize')))
if strcmpi(BPnotch,'on'),
boxplot(final_res, 'notch', 'on', ...
if strcmpi(BPnotch,'on')
boxplot(final_res, ...
'notch', 'on', ...
'positions', pos,...
'widths', wid)
elseif strcmpi(BPnotch,'off'),
boxplot(final_res, 'notch', 'off', ...
boxplot(final_res, ...
'notch', 'off', ...
'positions', pos,...
'widths', wid)
end
@@ -256,20 +243,20 @@ rotation= userPars.BProt;
ylim([-.5 (Lmax+10)])
ylabel('L in Hours', 'FontSize', fontSize)
%x-labels
% x-labels
text_h=findobj(gca, 'Type', 'text');
%rotation=45;
% rotation=45;
for cnt=1:length(text_h)
set(text_h(cnt), 'FontSize', fontSize,...
set(text_h(cnt), ...
'FontSize', fontSize,...
'Rotation', rotation, ...
'String', tickLabelStr{length(tickLabelStr)-cnt+1}, ...
'HorizontalAlignment', 'right')
end
% 'VerticalAlignment', 'cap', ...
% smaller box for axes, in order to un-hide the labels
% Smaller box for axes, in order to un-hide the labels
squeeze=0.2;
left=0.02;
right=1;
@@ -277,7 +264,7 @@ rotation= userPars.BProt;
top=1-squeeze;
set(gca, 'OuterPosition', [left bottom right top])
% remove outliers
% Remove outliers
hout=findobj(gca,'tag','Outliers');
for out_cnt=1 : length(hout)
if strcmpi(BPoutliers,'on'),
@@ -286,96 +273,84 @@ rotation= userPars.BProt;
set(hout(out_cnt), 'Visible', 'off')
end
end
end
end %if userlPars.boxplotFlg==1
% END OF BOX PLOT CODE****************************************************
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%*****************PLOT OVERLAY CODE**************************************
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%++++++++PLOT OVERLAY OF TRENDS FOR CHRONO OR DRUG-MEDIA PERMUTATIONS++++++++
% Plot Overlay Code
% Plot Overlay Of Trends For Chrono Or Drug-Media Permutations
try
lnwidth= str2num(Exp(4).plotPars{1});
axisFontSz= str2num(Exp(4).plotPars{2});
legFontSz= str2num(Exp(4).plotPars{3});
markerSz= str2num(Exp(4).plotPars{4});
lnwidth=str2num(Exp(4).plotPars{1});
axisFontSz=str2num(Exp(4).plotPars{2});
legFontSz=str2num(Exp(4).plotPars{3});
markerSz=str2num(Exp(4).plotPars{4});
catch
lnwidth=4;
axisFontSz=36;
legFontSz= 10;
legFontSz=10;
markerSz=5;
end
if userPars.boxplotFlg~=1 %PLOT OVERLAY OF TRENDS
if userPars.boxplotFlg~=1 % PLOT OVERLAY OF TRENDS
figure
set(gcf,'OuterPosition',(get(0,'screensize')))
if strcmp(Exp(expN).DexpType, 'chrono') %Chrono
%Plot median values for each DAY of the selected Trace
%(Gene-Specifics)using single DM of trace
if strcmp(Exp(expN).DexpType, 'chrono') % Chrono
% Plot median values for each DAY of the selected Trace
% (Gene-Specifics)using single DM of trace
range=0;
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
%trcInd= 0;
scnt= '['; %Init for Sample Count String
for trc=1:Exp(expN).traceN % length(Exp(expN).Trace)
% trcInd=0;
scnt='['; % Init for Sample Count String
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
for n=1:length(Exp(expN).Dexp) % LOOP Thru DayExps
tmp=[];
try
%if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
dmSel= Exp(expN).Trace(trc).dmSel;
dmSel=Exp(expN).Trace(trc).dmSel;
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
kFiltrIndx= find((cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<= kfiltLim);
tmp= cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayMed(trc,n)= median(tmp(kFiltrIndx)); %median(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
dayStd(trc,n)= std(tmp(kFiltrIndx)); %std(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
cnt= length(kFiltrIndx); %length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
kFiltrIndx=find((cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<=kfiltLim);
tmp=cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayMed(trc,n)=median(tmp(kFiltrIndx)); % median(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
dayStd(trc,n)=std(tmp(kFiltrIndx)); % std(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
cnt=length(kFiltrIndx); % length(cell2mat(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals));
else
kFiltrIndx= find(((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<= kfiltLim);
tmp= (Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayMed(trc,n)= median(tmp(kFiltrIndx)); %median(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayStd(trc,n)= std(tmp(kFiltrIndx)); %std(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
cnt= length(kFiltrIndx); %length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
kFiltrIndx=find(((Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrKvals))<=kfiltLim);
tmp=(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayMed(trc,n)=median(tmp(kFiltrIndx)); %median(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
dayStd(trc,n)=std(tmp(kFiltrIndx)); %std(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
cnt=length(kFiltrIndx); %length(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals);
end
%*************Make LEGEND list ********************************
%Make Sample Count Label item;
% Make LEGEND list
% Make Sample Count Label item;
if n~=length(Exp(expN).Dexp)
scnt= strcat(scnt,num2str(cnt),',');
scnt=strcat(scnt,num2str(cnt),',');
else
scnt= strcat(scnt,num2str(cnt),']');
scnt=strcat(scnt,num2str(cnt),']');
end
%Get Agar DrugMedia;
dm= Exp(expN).Trace(trc).dmSel;
drug= Exp(expN).Dexp(n).DM.drug{dm};
conc= Exp(expN).Dexp(n).DM.conc{dm};
media= Exp(expN).Dexp(n).DM.media{dm};
mod1= Exp(expN).Dexp(n).DM.mod1{dm};
conc1= Exp(expN).Dexp(n).DM.conc1{dm};
mod2= Exp(expN).Dexp(n).DM.mod2{dm};
dm=Exp(expN).Trace(trc).dmSel;
drug=Exp(expN).Dexp(n).DM.drug{dm};
conc=Exp(expN).Dexp(n).DM.conc{dm};
media=Exp(expN).Dexp(n).DM.media{dm};
mod1=Exp(expN).Dexp(n).DM.mod1{dm};
conc1=Exp(expN).Dexp(n).DM.conc1{dm};
mod2=Exp(expN).Dexp(n).DM.mod2{dm};
conc2=Exp(expN).Dexp(n).DM.conc2{dm};
dmStr= strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
NmLst(trc)= strcat(Exp(expN).Trace(trc).UsrGLB, dmStr,scnt);
dmStr=strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
NmLst(trc)=strcat(Exp(expN).Trace(trc).UsrGLB, dmStr,scnt);
%Determine Actual Exp Day from the ExpDay folder
loc= strfind(Exp(expN).Dexp(n).ExpFoldr,'_D');
daystr= Exp(expN).Dexp(n).ExpFoldr((loc+2):end);
dayNums(n)= str2num(daystr);
%trcInd= trcInd+1;
loc=strfind(Exp(expN).Dexp(n).ExpFoldr,'_D');
daystr=Exp(expN).Dexp(n).ExpFoldr((loc+2):end);
dayNums(n)=str2num(daystr);
%trcInd=trcInd+1;
catch
end
try
try
upperStd(trc,n)=dayMed(trc,n) + dayStd(trc,n);
lowerStd(trc,n)=dayMed(trc,n) - dayStd(trc,n);
catch
end
end %for n=1:length(Exp(expN).Dexp)
% end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
%Plot Trend Data
catch
end
end
% end
% Plot Trend Data
% if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
try
if iscell(Exp(expN).Trace(trc).Dexp(n).DM(dmSel).UsrLvals)
@@ -383,42 +358,39 @@ end
linecolor(trc)={get(hTrendFig,'color')};
else
clear NmLstStr
if iscell(NmLst(trc)),NmLstStr= cell2mat(NmLst(trc)); else NmLstStr= NmLstStr(trc); end
if isequal(NmLstStr(4:6),'cmp') ||...
isequal(NmLstStr(3:6),'cmpG') || ...
isequal(NmLstStr(3:6),'cmpP'),
if iscell(NmLst(trc)),NmLstStr=cell2mat(NmLst(trc)); else NmLstStr=NmLstStr(trc); end
if isequal(NmLstStr(4:6),'cmp') ||
|| isequal(NmLstStr(3:6),'cmpG') ...
|| isequal(NmLstStr(3:6),'cmpP')
hTrendFig=plot(dayNums,dayMed(trc,1:n),'lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
else
hTrendFig=plot(dayNums,dayMed(trc,1:n),'marker','^','lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
end
%yTicks= get(gca,'yTickLabel'); Ydelta= max(max(yTicks))-min(min(yTicks));
%spacing= Ydelta* 0.0034; %line spacing for STD marker
% yTicks=get(gca,'yTickLabel'); Ydelta=max(max(yTicks))-min(min(yTicks));
% spacing=Ydelta* 0.0034; %line spacing for STD marker
end
catch
hTrendFig=plot(1:n,dayMed(trc,1:n),'lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
ylabel('Experiment Day Index')
end %try
end % if isequal(get(Exp(expN).hOL(trc),'Visible'),'on') approx ln322
end
end
grid on
%set(gca,'linewidth',4) %0.5 then 1.5 now 6
%set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
% set(gca,'linewidth',4) %0.5 then 1.5 now 6
% set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
hold all
try % if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
tmpRange= ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
range= max(range,tmpRange);
catch,end
end %for trc= 1:Exp(expN).traceN approx. ln319
tmpRange=ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
range=max(range,tmpRange);
catch, end
end
%************** Standard Deviation range bars *****************************
% range= ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
spacing= range*0.0034; %marker splacing for building range bars
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
% Standard Deviation range bars
% range=ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
spacing=range*0.0034; %marker splacing for building range bars
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
for n=1:length(Exp(expN).Dexp) %LOOP Thru DayExps
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
@@ -426,169 +398,152 @@ for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
line(dayNums(n),lowerStd(trc,n):spacing:(dayMed(trc,n)-.05),'marker','^','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
line(dayNums(n),(dayMed(trc,n)+0.05):spacing:upperStd(trc,n),'marker','v','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
catch
%line(n,lowerStd(trc,n):0.05:(dayMed(trc,n)-.1),'marker','^','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
%line(n,(dayMed(trc,n)+0.1):0.05:upperStd(trc,n),'marker','v','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
% line(n,lowerStd(trc,n):0.05:(dayMed(trc,n)-.1),'marker','^','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
% line(n,(dayMed(trc,n)+0.1):0.05:upperStd(trc,n),'marker','v','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
end
end
end %for n=1:length(Exp(expN).Dexp)
end % if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
end %for trc= 1:Exp(expN).traceN
%legName=strrep(NmLst,'_','-');
mm=1;
for nn= 1:length(NmLst)
end
end
end
% legName=strrep(NmLst,'_','-');
mm=1;
for nn=1:length(NmLst)
if iscellstr(NmLst(nn))
legName(mm)=strrep(NmLst(nn),'_','-');
mm=mm+1;
end
end
legName =strrep(legName,'/','-');
end
legName=strrep(legName,'/','-');
hleg=legend((legName),'location','NEO');
set(hleg,'fontsize',legFontSz)
end
xlabel('Days')
ylabel('L in Hours')
title('Chronological Trend Plot with Standard Deviations')
hold off
%***************************************************************
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% Single or Multi Experiment
%***************************************************************
%SINGLE or MULTI-Experiment
if ~strcmp(Exp(expN).DexpType, 'chrono') %Single or Multi-Experiment
%Plot median values for each DM of the selected Trace (Gene-DM)
%(Gene-Specifics)using single DAY of trace
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
trcInd= 0;
DexpN= Exp(expN).Trace(trc).DexpN;
expFolder= Exp(expN).Dexp(DexpN).ExpFoldr;
if ~strcmp(Exp(expN).DexpType, 'chrono') %Single or Multi-Experiment
% Plot median values for each DM of the selected Trace (Gene-DM)
% (Gene-Specifics)using single DAY of trace
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
trcInd=0;
DexpN=Exp(expN).Trace(trc).DexpN;
expFolder=Exp(expN).Dexp(DexpN).ExpFoldr;
if ispc
lastSlash= max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '\'));
lastSlash=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '\'));
else
lastSlash= max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '/'));
lastSlash=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '/'));
end
expName= expFolder(lastSlash+1:end);
expName=expFolder(lastSlash+1:end);
if length(expName)>18
expNm= strcat('-',expName(1:18));
expNm=strcat('-',expName(1:18));
else
expNm= strcat('-',expName);
expNm=strcat('-',expName);
end
scnt= '['; %Init for Sample Count String
scnt='['; %Init for Sample Count String
for n=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru Drug-Media perturbations
tmp=[];
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
if iscell(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals)
kFiltrIndx= find((cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrKvals))<= kfiltLim);
tmp= (cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmMed(trc,n)= median(tmp(kFiltrIndx)); %median(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmStd(trc,n)= std(tmp(kFiltrIndx)); %std(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
cnt= length(kFiltrIndx); %length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
kFiltrIndx=find((cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrKvals))<=kfiltLim);
tmp=(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmMed(trc,n)=median(tmp(kFiltrIndx)); %median(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmStd(trc,n)=std(tmp(kFiltrIndx)); %std(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
cnt=length(kFiltrIndx); %length(cell2mat(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
else
kFiltrIndx= find(((Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrKvals))<= kfiltLim);
tmp= ((Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmMed(trc,n)= median(tmp(kFiltrIndx)); %median(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
dmStd(trc,n)= std(tmp(kFiltrIndx)); %std(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
cnt= length(kFiltrIndx); %length(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
kFiltrIndx=find(((Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrKvals))<=kfiltLim);
tmp=((Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals));
dmMed(trc,n)=median(tmp(kFiltrIndx)); %median(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
dmStd(trc,n)=std(tmp(kFiltrIndx)); %std(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
cnt=length(kFiltrIndx); %length(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals);
end
%*************Make LEGEND list ********************************
%Make Sample Count Label item
if n~=length(Exp(expN).Dexp(DexpN).DM.drug)
scnt= strcat(scnt,num2str(cnt),',');
else
scnt= strcat(scnt,num2str(cnt),']');
end
%Get Agar DrugMedia
drug= Exp(expN).Dexp(DexpN).DM.drug{n};
conc= Exp(expN).Dexp(DexpN).DM.conc{n};
media= Exp(expN).Dexp(DexpN).DM.media{n};
mod1= Exp(expN).Dexp(DexpN).DM.mod1{n};
conc1= Exp(expN).Dexp(DexpN).DM.conc1{n};
mod2= Exp(expN).Dexp(DexpN).DM.mod2{n};
conc2=Exp(expN).Dexp(DexpN).DM.conc2{n};
dmStr= strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
NmLst(trc)= strcat(Exp(expN).Trace(trc).UsrGLB, expNm,scnt);
trcInd= trcInd+1;
% Make Legend list
% Make Sample Count Label item
if n~=length(Exp(expN).Dexp(DexpN).DM.drug)
scnt=strcat(scnt,num2str(cnt),',');
else
scnt=strcat(scnt,num2str(cnt),']');
end
% Get Agar DrugMedia
drug=Exp(expN).Dexp(DexpN).DM.drug{n};
conc=Exp(expN).Dexp(DexpN).DM.conc{n};
media=Exp(expN).Dexp(DexpN).DM.media{n};
mod1=Exp(expN).Dexp(DexpN).DM.mod1{n};
conc1=Exp(expN).Dexp(DexpN).DM.conc1{n};
mod2=Exp(expN).Dexp(DexpN).DM.mod2{n};
conc2=Exp(expN).Dexp(DexpN).DM.conc2{n};
dmStr=strcat(drug,'_',conc,'_',media,'_',mod1,conc1,mod2,conc2);
NmLst(trc)=strcat(Exp(expN).Trace(trc).UsrGLB, expNm,scnt);
trcInd=trcInd+1;
upperStd(trc,n)=dmMed(trc,n) + dmStd(trc,n);
lowerStd(trc,n)=dmMed(trc,n) - dmStd(trc,n);
end %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
end
end
end %for n=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru Drug-Media perturbations
%Plot Trend Data
% Plot Trend Data
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
if iscell(Exp(expN).Trace(trc).Dexp(DexpN).DM(n).UsrLvals)
hTrendFig=plot(1:n,dmMed(trc,1:n),'lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
else
clear NmLstStr
if iscell(NmLst(trc)),NmLstStr= cell2mat(NmLst(trc)); else NmLstStr= NmLst(trc); end
if isequal(NmLstStr(4:6),'cmp') ||...
isequal(NmLstStr(3:6),'cmpG') || ...
isequal(NmLstStr(3:6),'cmpP'),
if iscell(NmLst(trc)),NmLstStr=cell2mat(NmLst(trc)); else NmLstStr=NmLst(trc); end
if isequal(NmLstStr(4:6),'cmp'), ...
|| isequal(NmLstStr(3:6),'cmpG'), ...
|| isequal(NmLstStr(3:6),'cmpP')
hTrendFig=plot(1:n,dmMed(trc,1:n),'lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
else
hTrendFig=plot(1:n,dmMed(trc,1:n),'marker','^','lineWidth',2); hold on
linecolor(trc)={get(hTrendFig,'color')};
end
end
% yTicks= get(gca,'yTickLabel'); Ydelta= max(max(yTicks))-min(min(yTicks));
%spacing= Ydelta* 0.0034; %line spacing for STD marker
% yTicks=get(gca,'yTickLabel'); Ydelta=max(max(yTicks))-min(min(yTicks));
% spacing=Ydelta* 0.0034; %line spacing for STD marker
end
grid on
%set(gca,'linewidth',4) %0.5 then 1.5 now 6
%set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
% set(gca,'linewidth',4) %0.5 then 1.5 now 6
% set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
hold all
end %for trc= 1:Exp(expN).traceN
end
%************** Standard Deviation range bars *****************************
%range= ceil(max(max(upperStd))) - floor(min(min(lowerStd)));
range= ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
spacing= range*0.0034;
for trc= 1:Exp(expN).traceN %length(Exp(expN).Trace)
% Standard Deviation range bars
% range=ceil(max(max(upperStd))) - floor(min(min(lowerStd)));
range=ceil(max(upperStd(trc,1:end))) - floor(min(lowerStd(trc,1:end)));
spacing=range*0.0034;
for trc=1:Exp(expN).traceN %length(Exp(expN).Trace)
for n=1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru Drug-Media perturbations
if isequal(get(Exp(expN).hOL(trc),'Visible'),'on')
try
line(n,lowerStd(trc,n):spacing:(dmMed(trc,n)-.05),'marker','^','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
line(n,(dmMed(trc,n)+0.05):spacing:upperStd(trc,n),'marker','v','LineWidth',1,'markerEdgeColor',cell2mat(linecolor(trc))); hold on
catch
end
end
end %for n=1:length(Exp(expN).Dexp)
end %for trc= 1:Exp(expN).traceN
end
end
mm=1;
for nn= 1:length(NmLst)
mm=1;
for nn=1:length(NmLst)
if iscellstr(NmLst(nn))
legName(mm)=strrep(NmLst(nn),'_','-');
mm=mm+1;
end
end
legName= strrep(legName,'/','-');
end
legName=strrep(legName,'/','-');
hleg=legend((legName),'location','NEO');
set(hleg,'fontsize',legFontSz)
xlabel('Drug-Media Index')
ylabel('L in Hours')
title('Drug-Media Trend Plot with Standard Deviations')
hold off
end %if ~strcmp(Exp(expN).DexpType, 'chrono') %Single or Multi-Experiment 395
%***************************************************************
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%end
end
hold off
end %if userPars.boxplotFlg~=1 %PLOT OVERLAY OF TRENDS 266

482
workflow/apps/matlab/ezview/EZhtMap.m
View File

@@ -8,12 +8,12 @@ if isempty(adj), adj=1.5; flip='T'; end
load('MyColormap1','modJet1')
load('MyColormap2','modJet2')
%load('MyColormap2','modJet0')
%adj= 1.5;
%adj=1.5;
cleanPallet=zeros(24,16);
if expN==1,DexpN= (get(handles.DN1,'value')); end
if expN==2,DexpN= (get(handles.DN2,'value')); end
if expN==3,DexpN= (get(handles.DN3,'value')); end
Exp(expN).DexpN=DexpN;
if expN==1,DexpN=(get(handles.DN1,'value')); end
if expN==2,DexpN=(get(handles.DN2,'value')); end
if expN==3,DexpN=(get(handles.DN3,'value')); end
Exp(expN).DexpN=DexpN;
try
if expN==1,MPsel=floor(get(ghandles.MPsldr1,'value')); end
if expN==2,MPsel=floor(get(ghandles.MPsldr2,'value')); end
@@ -30,42 +30,50 @@ if expN==1, expAxes=ghandles.Iaxes1;end
if expN==2, expAxes=ghandles.Iaxes2;end
if expN==3, expAxes=ghandles.Iaxes3;end
dmN= length(Exp(expN).Dexp(DexpN).DM.drug);
mpSel= Exp(expN).Dexp(DexpN).MPsel;
dmSel= Exp(expN).Dexp(DexpN).pertSel;
scnN= dmSel + (dmN*(mpSel-1));
dmN=length(Exp(expN).Dexp(DexpN).DM.drug);
mpSel=Exp(expN).Dexp(DexpN).MPsel;
dmSel=Exp(expN).Dexp(DexpN).pertSel;
scnN=dmSel + (dmN*(mpSel-1));
if expN==1,htTog= Exp(1).htmapPBsel;end
if expN==2,htTog= Exp(2).htmapPBsel;end
if expN==3,htTog= Exp(3).htmapPBsel;end
if expN==1,htTog=Exp(1).htmapPBsel;end
if expN==2,htTog=Exp(2).htmapPBsel;end
if expN==3,htTog=Exp(3).htmapPBsel;end
%00000000 LLLLLLLLLLLLLL 00000000000000000000000000000000000000000000000
if htTog==0
colormap(flipud(modJet1)) %colormap(modJet2)
L= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,5);
L=reshape(L,24,16);
LpStd= mean(nonzeros(L(:)))+(adj*std(nonzeros(L(:))));
LnStd= mean(nonzeros(L(:))-(adj*std(nonzeros(L(:)))));
%Data rescaling for Heatmap display (color range- mean+/std*adjustment)
for i=1:size(L,1)
colormap(flipud(modJet1)) % colormap(modJet2)
L=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,5);
L=reshape(L,24,16);
LpStd=mean(nonzeros(L(:)))+(adj*std(nonzeros(L(:))));
LnStd=mean(nonzeros(L(:))-(adj*std(nonzeros(L(:)))));
% Data rescaling for Heatmap display (color range- mean+/std*adjustment)
for i=1:size(L,1)
for j=1:size(L,2)
if L(i,j)>LpStd,
L4hMap(i,j)= LpStd;
L4hMap(i,j)=LpStd;
elseif L(i,j)<LnStd && L(i,j)~=0
L4hMap(i,j)= LnStd;
elseif L(i,j)== 0
L4hMap(i,j)= LpStd+0.2*std(L(:));
L4hMap(i,j)=LnStd;
elseif L(i,j)==0
L4hMap(i,j)=LpStd+0.2*std(L(:));
else
L4hMap(i,j)= L(i,j);
L4hMap(i,j)=L(i,j);
end
end
end
%L4hMap= 1-(L4hMap/(max(L4hMap(:))));
%---------------------------------------------------
if prntHt== 0
hTogHt= figure;
end
% L4hMap=1-(L4hMap/(max(L4hMap(:))));
if prntHt==0
hTogHt=figure;
h=image(cleanPallet); % hTogHt=image(cleanPallet);
h=image(L4hMap); % hTogHt=image(L4hMap);
if isequal(char(flip) , 'T')
colormap(flipud(modJet1)) %(flipud(hot)) %(jet); % invert heat map for L so that fastgrowth is 'hotter' red
else
colormap(modJet2)
end
set(h,'CDataMapping','scale') %set(hTogHt,'CDataMapping','scale')
else
figure
h=image(cleanPallet); %hTogHt=image(cleanPallet);
h=image(L4hMap); %hTogHt=image(L4hMap);
if isequal(char(flip) , 'T')
@@ -73,173 +81,155 @@ if prntHt== 0
else
colormap(modJet2)
end
set(h,'CDataMapping','scale') %set(hTogHt,'CDataMapping','scale')
else
figure
h= image(cleanPallet); %hTogHt= image(cleanPallet);
h=image(L4hMap); %hTogHt=image(L4hMap);
if isequal(char(flip) , 'T')
colormap(flipud(modJet1)) %(flipud(hot)) %(jet); % invert heat map for L so that fastgrowth is 'hotter' red
else
colormap(modJet2)
end
set(h,'CDataMapping','scale')
end
end
%h=image(L);
%colormap(flipud(hot)) %(jet); % invert heat map for L so that fastgrowth is 'hotter' red
%set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
% h=image(L);
% colormap(flipud(hot)) %(jet); % invert heat map for L so that fastgrowth is 'hotter' red
% set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt== 0
if prntHt==0
%if expN==1,cla(handles.HtMap1);copyobj(hTogHt,ghandles.HtMap1);end
%if expN==2,cla(handles.HtMap2);copyobj(hTogHt,ghandles.HtMap2);end
%if expN==3,cla(handles.HtMap3);copyobj(hTogHt,ghandles.HtMap3);end
close(hTogHt)
else %if clicking to produce a 'printable' save display
else %if clicking to produce a 'printable' save display
set(gca,'XDir','reverse')
set(gca,'XTickMode','manual')
%set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
%set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
%set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
colorbar
expLblHtmap= Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap= char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
expLblHtmap=Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap=char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
title({strcat('L HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
colormap(modJet1) %Fix added 230814
%3333333333 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
end
colormap(modJet1)
elseif htTog==1
colormap(modJet1);
K= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,3);
K=reshape(K,24,16);
%Data rescaling for Heatmap display (color ranged mean+/std*multiplier)
pStd= mean(nonzeros(K(:)))+(adj*std(nonzeros(K(:))));
nStd= mean(nonzeros(K(:)))-(adj*std(nonzeros(K(:))));
for i=1:size(K,1)
colormap(modJet1);
K=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,3);
K=reshape(K,24,16);
%Data rescaling for Heatmap display (color ranged mean+/std*multiplier)
pStd=mean(nonzeros(K(:)))+(adj*std(nonzeros(K(:))));
nStd=mean(nonzeros(K(:)))-(adj*std(nonzeros(K(:))));
for i=1:size(K,1)
for j=1:size(K,2)
if K(i,j)>pStd,
hMap(i,j)= pStd;
hMap(i,j)=pStd;
elseif K(i,j)<nStd && K(i,j)~=0
hMap(i,j)= nStd;
elseif K(i,j)== 0
hMap(i,j)= nStd-0.2*std(K(:));
hMap(i,j)=nStd;
elseif K(i,j)==0
hMap(i,j)=nStd-0.2*std(K(:));
else
hMap(i,j)= K(i,j);
hMap(i,j)=K(i,j);
end
end
end
end
%---------------------------------------------------
if prntHt== 0
hTogHt= figure;
h=image(cleanPallet);
else
figure
h= image(cleanPallet);
end
%h=image(cleanPallet);
h=image(hMap);
colormap(modJet1); % heat map
set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt== 0
if prntHt==0
hTogHt=figure;
h=image(cleanPallet);
else
figure
h=image(cleanPallet);
end
% h=image(cleanPallet);
h=image(hMap);
colormap(modJet1); % heat map
set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt==0
close(hTogHt)
else
else
set(gca,'XDir','reverse')
set(gca,'XTickMode','manual')
%set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
%set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
%set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
colorbar
expLblHtmap= Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap= char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
expLblHtmap=Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap=char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
title({strcat('K HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
%444444444 rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr
end
elseif htTog==2
colormap(modJet1);
r= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,4);
r=reshape(r,24,16);
%Data rescaling for Heatmap display (color ranged mean+/std*multiplier)
pStd= mean(nonzeros(r(:)))+(adj*std(nonzeros(r(:))));
nStd= mean(nonzeros(r(:)))-(adj*std(nonzeros(r(:))));
for i=1:size(r,1)
colormap(modJet1);
r=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(:,4);
r=reshape(r,24,16);
% Data rescaling for Heatmap display (color ranged mean+/std*multiplier)
pStd=mean(nonzeros(r(:)))+(adj*std(nonzeros(r(:))));
nStd=mean(nonzeros(r(:)))-(adj*std(nonzeros(r(:))));
for i=1:size(r,1)
for j=1:size(r,2)
if r(i,j)>pStd,
hMap(i,j)= pStd;
hMap(i,j)=pStd;
elseif r(i,j)<nStd && r(i,j)~=0,
hMap(i,j)= nStd;
elseif r(i,j)== 0
hMap(i,j)= nStd-0.2*std(r(:));
hMap(i,j)=nStd;
elseif r(i,j)==0
hMap(i,j)=nStd-0.2*std(r(:));
else
hMap(i,j)= r(i,j);
hMap(i,j)=r(i,j);
end
end
end
%---------------------------------------------------
if prntHt== 0
hTogHt= figure;
end
if prntHt==0
hTogHt=figure;
h=image(cleanPallet);
else
else
figure
h= image(cleanPallet);
end
%h=image(cleanPallet);
h=image(hMap);
colormap(modJet1); % heat map
set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt== 0
h=image(cleanPallet);
end
% h=image(cleanPallet);
h=image(hMap);
colormap(modJet1); % heat map
set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt==0
close(hTogHt)
else
else
set(gca,'XDir','reverse')
set(gca,'XTickMode','manual')
%set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
%set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
%set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
colorbar
expLblHtmap= Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap= char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
expLblHtmap=Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap=char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
title({strcat('r HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
%33333333333333333333333333333333333333333333333333333(1111111111111111111)
end
elseif htTog==3
RFconfig=Exp(expN).RFconfig; %ZoneRelated
if htMapTogPBfg==1
if RFconfig==2,
QctrlRF= 'Select Distributed Control RF option: (G)Global, (L)Local';
QpertRF= 'Select Distributed Perturbation RF option: (G)Global, (L)Local';
defaultanswer= {'G','L'}; %{'80','60','100','3,4,5','N','39','Y','G','L'};
try defaultanswer= Exp(expN).htmapRFanswer; catch, defaultanswer= {'G','L'};end %ZoneRelated
QctrlRF='Select Distributed Control RF option: (G)Global, (L)Local';
QpertRF='Select Distributed Perturbation RF option: (G)Global, (L)Local';
defaultanswer={'G','L'}; %{'80','60','100','3,4,5','N','39','Y','G','L'};
try defaultanswer=Exp(expN).htmapRFanswer; catch, defaultanswer={'G','L'};end %ZoneRelated
end
if RFconfig==3,
QctrlRF= 'Select Control RF option: (F)FullPlate, (G)GlobalDistributed, (L)LocalDistributed';
QpertRF= 'Select Perturbation RF option: (F)FullPlate, (G)GlobalDistributed, (L)LocalDistributed';
QctrlRF='Select Control RF option: (F)FullPlate, (G)GlobalDistributed, (L)LocalDistributed';
QpertRF='Select Perturbation RF option: (F)FullPlate, (G)GlobalDistributed, (L)LocalDistributed';
defaultanswer={'F','L'}; %{'80','60','100','3,4,5','N','39','Y','F','L'};
try defaultanswer= Exp(expN).htmapRFanswer; catch, defaultanswer= {'F','L'}; end %ZoneRelated
try defaultanswer=Exp(expN).htmapRFanswer; catch, defaultanswer={'F','L'}; end %ZoneRelated
end
if RFconfig~=1,
prompt={
QctrlRF,...
QpertRF,...
};
prompt={QctrlRF,QpertRF};
name='Interaction User Input';
numlines=1;
answer=inputdlg(prompt,name,numlines,defaultanswer);
@@ -251,151 +241,137 @@ elseif htTog==3
if ~ismember(answer{1},['f' 'F' 'g' 'G' 'l' 'L']), answer(1)=defaultanswer(1); end
if ~ismember(answer{2},['f' 'F' 'g' 'G' 'l' 'L']), answer(2)=defaultanswer(2); end
end
answer(1)= strrep(answer(1),'f','F'); answer(1)= strrep(answer(1),'g','G'); answer(1)= strrep(answer(1),'l','L');
answer(2)= strrep(answer(2),'f','F'); answer(2)= strrep(answer(2),'g','G'); answer(2)= strrep(answer(2),'l','L');
Exp(expN).htmapRFanswer= answer; %ZoneRelated %store user last selections
answer(1)=strrep(answer(1),'f','F'); answer(1)=strrep(answer(1),'g','G'); answer(1)=strrep(answer(1),'l','L');
answer(2)=strrep(answer(2),'f','F'); answer(2)=strrep(answer(2),'g','G'); answer(2)=strrep(answer(2),'l','L');
Exp(expN).htmapRFanswer=answer; %ZoneRelated %store user last selections
end
end
end %if htMapTogPBfg==1
htMapTogPBfg=0;
answer= Exp(expN).htmapRFanswer; %ZoneRelated
answer=Exp(expN).htmapRFanswer; %ZoneRelated
%for j=1:1 %dmN
% for m=1:1 %mpN
% for j=1:1 %dmN
% for m=1:1 %mpN
j=dmSel;
DM0= dmSel; DMj= dmSel;
m= mpSel;
%****************
anN= [1 2]; %*
EZintRFs %* Call subroutine to interpret user RF inputs & det. Rn and Rs values
%****************
scnNdm1= 1 + (dmN*(m-1))
scnN= j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..;
Xn{m,j,1}= [];
Xln{m,j,1}= [];
Xhn{m,j,1}= [];
DM0=dmSel; DMj=dmSel;
m=mpSel;
anN=[1 2];
% Call subroutine to interpret user RF inputs & det. Rn and Rs values
EZintRFs
scnNdm1=1 + (dmN*(m-1))
scnN=j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..;
Xn{m,j,1}=[];
Xln{m,j,1}=[];
Xhn{m,j,1}=[];
Xn{m,1,:}=Exp(expN).Dexp(DexpN).scan(scnNdm1).plate(1).CFout(:,5);
Xln{m,1,:}=Exp(expN).Dexp(DexpN).scan(scnNdm1).plate(1).CFout(:,11); %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,11);
Xhn{m,1,:}=Exp(expN).Dexp(DexpN).scan(scnNdm1).plate(1).CFout(:,12); %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,12);
Xn{m,j,:}=Exp(expN).Dexp(DexpN).scan(scnN).plate(1).CFout(:,5); %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,5);
htmpCpyXn=Xn{m,j,:}'; % Use to find and delineate no growth spots with 999 in text field (infinite interaction) value;
Xn{m,j,:}(Xn{m,j,:}==0)= 1.2*(max(Xn{m,j,:})); %to keep the colormap scale tighter %=140;
Xn{m,j,:}(Xn{m,j,:}==0)=1.2*(max(Xn{m,j,:})); %to keep the colormap scale tighter %=140;
Xln{m,j,:}=Exp(expN).Dexp(DexpN).scan(scnN).plate(1).CFout(:,11); %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,11);
Xhn{m,j,:}=Exp(expN).Dexp(DexpN).scan(scnN).plate(1).CFout(:,12); %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,12);
%*********************************************************
%intL{m,j,:}= ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
intL= ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
%intL{m,j,:}=((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
intL=((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
Exp(expN).HtMpIntN2=intL; %ZoneRelated
%{
intL{m,j,:}(Xn{m,j,:}==1.2*(max(Xn{m,j,:})))= 100;
intL{m,j,:}(Xn{m,j,:}==1.2*(max(Xn{m,j,:})))=100;
intL{m,j,:}(intL{m,j,:}==0)=-0.0001;
%}
percentRs= 100;
RsReduced(j)= percentRs/100* Rs(j);
deltaRp(j)= (Rn(j)+RsReduced(j))-(Rn(1)+RsReduced(1));
percentRs=100;
RsReduced(j)=percentRs/100* Rs(j);
deltaRp(j)=(Rn(j)+RsReduced(j))-(Rn(1)+RsReduced(1));
deltaRn(j)=(Rn(j)-RsReduced(j))-(Rn(1)-RsReduced(1));
if deltaRp(j)==0, deltaRp(j)=0.0002; end
if deltaRn(j)==0, deltaRn(j)=0.0002; end
deltaYp= zeros(1,384); deltaYn= zeros(1,384);
deltaXRp= zeros(1,384); deltaXRn= zeros(1,384);
deltaXR{m,j}= zeros(1,384);
deltaYp=zeros(1,384); deltaYn=zeros(1,384);
deltaXRp=zeros(1,384); deltaXRn=zeros(1,384);
deltaXR{m,j}=zeros(1,384);
for i=1:384
%Select lower or upper boundary value based on Yn(1)
if Xn{m,j}(i) >= (Rn(j)+RsReduced(j));
% Select lower or upper boundary value based on Yn(1)
if Xn{m,j}(i) >=(Rn(j)+RsReduced(j));
deltaYp(i)= Xln{m,j}(i)-Xln{m,1}(i);
elseif Xn{m,j}(i) < (Rn(j)-RsReduced(j));
deltaYn(i)= Xhn{m,j}(i)-Xhn{m,1}(i);
% Insert else
end
%Calculate deltaXRp and deltaXRn for each plate based on growth relative to deltaRp or deltaRn
if deltaYp(i)>= deltaRp(j)
deltaXRp(i)= deltaYp(i)-deltaRp(j);
deltaXR{m,j}(i)= deltaXRp(i); %Consoludate into deltaXR{m,j}(i) cell array
% Calculate deltaXRp and deltaXRn for each plate based on growth relative to deltaRp or deltaRn
if deltaYp(i)>=deltaRp(j)
deltaXRp(i)=deltaYp(i)-deltaRp(j);
deltaXR{m,j}(i)=deltaXRp(i); %Consoludate into deltaXR{m,j}(i) cell array
elseif deltaYn(i) < deltaRn(j)
deltaXRn(i)= deltaYn(i)-deltaRn(j);
deltaXR{m,j}(i)= deltaXRn(i); %Consoludate into deltaXR{m,j}(i) cell array
deltaXRn(i)=deltaYn(i)-deltaRn(j);
deltaXR{m,j}(i)=deltaXRn(i); %Consoludate into deltaXR{m,j}(i) cell array
if deltaYn(i)==0, deltaXR{m,j}(i)=0; end
end
%Ambiguous results that have delta gene values that are less than the variance of Reference+/-std
end %for i=1:384
deltaXRl= deltaXR{m,j,:};
htMpN1Lzeros999= deltaXR{m,j,:};
% Ambiguous results that have delta gene values that are less than the variance of Reference+/-std
end
deltaXRl=deltaXR{m,j,:};
htMpN1Lzeros999=deltaXR{m,j,:};
deltaXRl(htmpCpyXn==0)=1.2*max(deltaXRl);
htMpN1Lzeros999(htmpCpyXn==0)=999;
Exp(expN).HtMpIntN1=htMpN1Lzeros999';
%**************************************************************************
I=reshape(deltaXRl,24,16);
if prntHt== 0
hTogHt= figure;
I=reshape(deltaXRl,24,16);
if prntHt==0
hTogHt=figure;
h=image(cleanPallet);
else
else
figure
h= image(cleanPallet);
end
%h=figure;
h=image(I);
colormap(jet); % heat map
set(h,'CDataMapping','scale')
h=image(cleanPallet);
end
% h=figure;
h=image(I);
colormap(jet); % heat map
set(h,'CDataMapping','scale')
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if expN==1,cla(handles.HtMap1);copyobj(h,ghandles.HtMap1);end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt== 0
if prntHt==0
close(hTogHt)
else
else
set(gca,'XDir','reverse')
set(gca,'XTickMode','manual')
%set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
%set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
%set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
% set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
% set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
% set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
colorbar
expLblHtmap= Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap= char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
expLblHtmap=Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap=char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
title({strcat('N1 HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
% end %for m=1:1
%end %for j=1:1
%4444444444444444444444444444444444444444444444444444444444(22222222222222222)
end
elseif htTog==4
answer= Exp(expN).htmapRFanswer; %ZoneRelated
RFconfig=Exp(expN).RFconfig; %ZoneRelated
answer= Exp(expN).htmapRFanswer; %ZoneRelated
answer=Exp(expN).htmapRFanswer; % ZoneRelated
RFconfig=Exp(expN).RFconfig; % ZoneRelated
answer=Exp(expN).htmapRFanswer; % ZoneRelated
j=dmSel;
DM0= dmSel; DMj= dmSel;
m= mpSel;
%****************
anN= [1 2]; %*
EZintRFs %* Call subroutine to interpret user RF inputs
%****************
scnNdm1= 1 + (dmN*(m-1))
scnN= j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..;
Xn{m,j,1}= [];
DM0=dmSel; DMj=dmSel;
m=mpSel;
anN=[1 2];
EZintRFs % Call subroutine to interpret user RF inputs
scnNdm1=1 + (dmN*(m-1))
scnN=j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..;
Xn{m,j,1}=[];
Xn{m,1,:}=Exp(expN).Dexp(DexpN).scan(scnNdm1).plate(1).CFout(:,5);
Xn{m,j,:}=Exp(expN).Dexp(DexpN).scan(scnN).plate(1).CFout(:,5);
htmpCpyXn=Xn{m,j,:}'; % Use to find and delineate no growth spots with 999 in text field (infinite interaction) value;
intL= ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
Exp(expN).HtMpIntN2=intL; %ZoneRelated
intL= Exp(expN).HtMpIntN2; %ZoneRelated
intL=((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
Exp(expN).HtMpIntN2=intL; % ZoneRelated
intL=Exp(expN).HtMpIntN2; % ZoneRelated
I=reshape(intL,24,16);
if prntHt== 0
hTogHt= figure;
if prntHt==0
hTogHt=figure;
h=image(cleanPallet);
elsef
elseif
figure
h= image(cleanPallet);
end
h=image(cleanPallet);
end
%h=figure
h=image(I)
colormap(jet); % heat map
@@ -404,24 +380,26 @@ end
if expN==2,cla(handles.HtMap2);copyobj(h,ghandles.HtMap2);end
if expN==3,cla(handles.HtMap3);copyobj(h,ghandles.HtMap3);end
if prntHt== 0
if prntHt==0
close(hTogHt)
else
set(gca,'XDir','reverse')
set(gca,'XTickMode','manual')
%set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
%set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
%set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
% set(gca,'XTickLabel',{'2';'4';'6';'8';'10';'12';'14';'16'})
% set(gca,'XTickLabel',{'16';'14';'12';'10';'8';'6';'4';'2'})
% set(gca,'XTick',{0;2;4;6;8;10;12;14;16;18})
colorbar
expLblHtmap= Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap= char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},...
' ',Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
expLblHtmap=Exp(expN).Dexp.ExpFoldr;
mediaLBhtmap=char(strcat(', Agar-',Exp(expN).Dexp(DexpN).DM.media{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.drug{pertSel},Exp(expN).Dexp(DexpN).DM.conc{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod1{pertSel},Exp(expN).Dexp(DexpN).DM.conc1{pertSel},' ',...
Exp(expN).Dexp(DexpN).DM.mod2{pertSel},Exp(expN).Dexp(DexpN).DM.conc2{pertSel}));
title({strcat('N2 HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
end
prntHt=0;
% Update htMapText for location on the first 'roll thru of htMapPB
EZhtMapText
end %if htTog==
prntHt= 0;
%************* *****
EZhtMapText %* Update htMapText for location on the first 'roll thru of htMapPB
%************* *****

125
workflow/apps/matlab/ezview/EZhtMapText.m
View File

@@ -1,82 +1,79 @@
%EZhtMapText.m
%*********************HeatMap Text Field*********************************
% HeatMap Text Field
try
indx=Exp(expN).Dexp(DexpN).spotIndx;
l= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,5);
k= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,3);
r= Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,4);
try
ll=num2str(l);
if length(ll)>5,htl= ll(1:5);else htl=ll;end
if ~isempty(htl), htl=strcat('_L=',htl);else htl=' ';end
catch
indx=Exp(expN).Dexp(DexpN).spotIndx;
l=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,5);
k=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,3);
r=Exp(expN).Dexp(DexpN).scan(scnN).plate.CFout(indx,4);
try
ll=num2str(l);
if length(ll)>5,htl=ll(1:5);else htl=ll;end
if ~isempty(htl), htl=strcat('_L=',htl);else htl=' ';end
catch
htl=' ';
end
end
try
kk=num2str(k);
if length(kk)>5,htk= kk(1:5);else htk=kk;end
if ~isempty(htk), htk=strcat('_K=',htk);else htk=' ';end
catch
try
kk=num2str(k);
if length(kk)>5,htk=kk(1:5);else htk=kk;end
if ~isempty(htk), htk=strcat('_K=',htk);else htk=' ';end
catch
htk=' ';
end
end
try
rr=num2str(r);
if length(rr)>5,htr= rr(1:5);else htr=rr;end
if ~isempty(htr), htr=strcat('_r=',htr);else htr=' ';end
catch
try
rr=num2str(r);
if length(rr)>5,htr=rr(1:5);else htr=rr;end
if ~isempty(htr), htr=strcat('_r=',htr);else htr=' ';end
catch
htr=' ';
end
end
try
n1= num2str(Exp(expN).HtMpIntN1(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1= n1(1:5);else N1=n1; end
try
n1=num2str(Exp(expN).HtMpIntN1(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1=n1(1:5);else N1=n1; end
if ~isempty(N1), htN1=strcat('_N1=',N1);else htN1=' ';end
catch
catch
htN1=' ';
end
end
try
n2= num2str(Exp(expN).HtMpIntN2(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN2(indx));
if length(n2)>5,N2= n2(1:5);else N2=n2; end
try
n2=num2str(Exp(expN).HtMpIntN2(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN2(indx));
if length(n2)>5,N2=n2(1:5);else N2=n2; end
if ~isempty(N2), htN2=strcat('_N2=',N2);else htN2=' ';end %htN2=strcat('_N2=',N2);
catch
catch
htN2=' ';
end
end
try
if htTog==0 || htTog> 2
htmapStr=strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
try
if htTog==0 || htTog> 2
htmapStr=strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
try
if htTog==1
htmapStr=htk %strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
try
if htTog==1
htmapStr=htk %strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
try
if htTog==2
htmapStr=htr %strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
try
if htTog==2
htmapStr=htr %strcat(htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
catch
end
catch
msg= 'No spot selected (indx=Exp(expN).Dexp(DexpN).spotIndx)'
msg='No spot selected (indx=Exp(expN).Dexp(DexpN).spotIndx)'
end

46
workflow/apps/matlab/ezview/EZintPrint.m
View File

@@ -1,6 +1,4 @@
%print Interaction Data Output file
%**************************************************************************************
%resDir=Exp(expN).Dexp(DexpN).resDir;
%expN=1; %temp entry
if strcmp(Exp(expN).DexpType, 'single') || strcmp(Exp(expN).DexpType,'multi')
@@ -14,7 +12,6 @@ elseif strcmp(Exp(expN).DexpType, 'chrono')
pertTypeLB= '; Dayselections:';
Rsmax=max(Rs(1),Rs(1:dmN));
%MKDIR for ChonologicalStudy results in Exp Group folder
%For chrono studies, put the interaction results in the first Exp of selected group. i.e., DexpN=1;
intLfilename1= fullfile(Exp(expN).Dexp(1).resDir,'PrintResults','!AggrevatingL-Chrono.txt');
intLfilename2= fullfile(Exp(expN).Dexp(1).resDir,'PrintResults','!AlleviatingL-Chrono.txt');
@@ -22,11 +19,11 @@ elseif strcmp(Exp(expN).DexpType, 'chrono')
intLfilename4= fullfile(Exp(expN).Dexp(1).resDir,'PrintResults','!AlleviatingLadjusted-Chrono.txt');
end
userInputs=cell2mat(strcat( 'ExpZone:',num2str(expN), '; LeftPercent',answer(1),'; RightPercent:',answer(2),'; RFstdPercent:',answer(3),pertTypeLB,answer(4),'; RemoveNoGrowthInfLs:',answer(5),...
'; NumberOfHistogramBins:',answer(6),'; Subplots:',answer(7))); %answer(7)
userInputs=cell2mat(strcat( 'ExpZone:',num2str(expN), '; LeftPercent',answer(1),'; RightPercent:',answer(2),...
'; RFstdPercent:',answer(3),pertTypeLB,answer(4),'; RemoveNoGrowthInfLs:',answer(5),...
'; NumberOfHistogramBins:',answer(6),'; Subplots:',answer(7))); %answer(7)
%********************11111111111111111111111111111111111111111****************************************************************************************************************
%Interaction Printout for Positive (longer L interaction values) Non-Adjusted for Ref std and curve fit boundaries
% Interaction Printout for Positive (longer L interaction values) Non-Adjusted for Ref std and curve fit boundaries
fid=fopen(intLfilename1,'w');
ln=1;
fprintf(fid,'%d\t',ln);
@@ -41,28 +38,27 @@ for j=1:length(DMsel), fprintf(fid,'%s\t',strcat('IntLdm',num2str(DMsel(j)))); e
fprintf(fid,'Specifics\tReplicate\tStrain\tMP\tRow\tCol\tIndex');
fprintf(fid, '\n');
if ~isempty(InterslstPos{1})
for i=1:size(selIntP,1)
for i=1:size(selIntP,1)
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'%s\t%s\t',cell2mat(IPorf(i)),cell2mat(IPgene(i)));
for j=1:length(DMsel) %'Scan\tPlate\tRow\tCol\t');
for j=1:length(DMsel) % 'Scan\tPlate\tRow\tCol\t');
fprintf(fid,'%.5f\t',IntersValsPos(i,j))
end
% fprintf(fid,'%.5f\t%.5f\t%.5f\t',ipL(i),ipLlower(i),ipLupper(i))
fprintf(fid,'%s\t%s\t%s\t',cell2mat(IPspecifics(i)),cell2mat(IPorfRep(i)),cell2mat(IPstrain(i)));
fprintf(fid,'%.5f\t%.5f\t%.5f\t',selIntPx{1}(i,2),selIntPx{1}(i,4),selIntPx{1}(i,5),InterslstPos{1}(i))
fprintf(fid, '\n');
end
end
else
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'%s\t','Empty Set, No interaction found within set range.');
end
% fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene\tAUC\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
% fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene\tAUC\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
fclose(fid)
%********************222222222222222222222222222222222222222222222****************************************************************************************************************
%Interaction Printout for Negative (shorter L interaction values) Non-Adjusted for Ref std and curve fit boundaries
% Interaction Printout for Negative (shorter L interaction values) Non-Adjusted for Ref std and curve fit boundaries
fid=fopen(intLfilename2,'w');
ln=1;
fprintf(fid,'%d\t',ln);
@@ -77,25 +73,23 @@ for j=1:length(DMsel), fprintf(fid,'%s\t',strcat('IntLdm',num2str(DMsel(j)))); e
fprintf(fid,'Specifics\tReplicate\tStrain\tMP\tRow\tCol\tIndex');
fprintf(fid, '\n');
if ~isempty(InterslstNeg{1})
for i=1:size(selIntN,1)
for i=1:size(selIntN,1)
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'%s\t%s\t',cell2mat(INorf(i)),cell2mat(INgene(i)));
for j=1:length(DMsel) %'Scan\tPlate\tRow\tCol\t');
for j=1:length(DMsel) % 'Scan\tPlate\tRow\tCol\t');
fprintf(fid,'%.5f\t',IntersValsNeg(i,j))
end
% fprintf(fid,'%.5f\t%.5f\t%.5f\t',ipL(i),ipLlower(i),ipLupper(i))
fprintf(fid,'%s\t%s\t%s\t',cell2mat(INspecifics(i)),cell2mat(INorfRep(i)),cell2mat(INstrain(i)));
fprintf(fid,'%.5f\t%.5f\t%.5f\t%.5f\t',selIntNx{1}(i,2),selIntNx{1}(i,4),selIntNx{1}(i,5),InterslstNeg{1}(i))
fprintf(fid, '\n');
end
end
end
fclose(fid)
%********************3333333333333333333333333333333333333333333333****************************************************************************************************************
%Interaction Printout for Positive (longer L interaction values) "ADJUSTED" for Ref std and curve fit boundaries
% Interaction Printout for Positive (longer L interaction values) "ADJUSTED" for Ref std and curve fit boundaries
fid=fopen(intLfilename3,'w');
ln=1;
fprintf(fid,'%d\t',ln);
@@ -106,7 +100,7 @@ ln=2;
fprintf(fid,'%d\t',ln);
fprintf(fid, 'Orf\tGene\t');
for j=1:length(DMsel), fprintf(fid,'%s\t',strcat('IntLdm',num2str(DMsel(j)))); end
%fprintf(fid, 'L\tLlower\tLupper\t')
% fprintf(fid, 'L\tLlower\tLupper\t')
fprintf(fid,'Specifics\tReplicate\tStrain\tMP\tRow\tCol\tIndex');
fprintf(fid, '\n');
for i=1:size(selIntPAdj,1)
@@ -120,14 +114,10 @@ for i=1:size(selIntPAdj,1)
fprintf(fid,'%s\t%s\t%s\t',cell2mat(IPspecificsAdj(i)),cell2mat(IPorfRepAdj(i)),cell2mat(IPstrainAdj(i)));
fprintf(fid,'%.5f\t%.5f\t%.5f\t',selIntPxAdj{1}(i,2),selIntPxAdj{1}(i,4),selIntPxAdj{1}(i,5),InterslstPosAdj{1}(i))
fprintf(fid, '\n');
end
% fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene\tAUC\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
% fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene\tAUC\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
fclose(fid)
%********************44444444444444444444444444444444444444444444****************************************************************************************************************%Interaction Printout for Negative (shorter L interaction values) Non-Adjusted for Ref std and curve fit boundaries
fid=fopen(intLfilename4,'w');
ln=1;
fprintf(fid,'%d\t',ln);
@@ -153,9 +143,7 @@ for i=1:size(selIntNAdj,1)
% fprintf(fid,'%.5f\t%.5f\t%.5f\t',ipL(i),ipLlower(i),ipLupper(i))
fprintf(fid,'%s\t%s\t%s\t',cell2mat(INspecificsAdj(i)),cell2mat(INorfRepAdj(i)),cell2mat(INstrainAdj(i)));
fprintf(fid,'%.5f\t%.5f\t%.5f\t',selIntNxAdj{1}(i,2),selIntNxAdj{1}(i,4),selIntNxAdj{1}(i,5),InterslstNegAdj{1}(i))
fprintf(fid, '\n');
end
end

84
workflow/apps/matlab/ezview/EZintRFs.m
View File

@@ -3,85 +3,85 @@ if RFconfig==1
end
if RFconfig==2
ctrlRF= cell2mat(answer(anN(1)))
ctrlRF=cell2mat(answer(anN(1)))
switch ctrlRF
case {'G','g'}
Rn(1)= Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstdG(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstdG(DM0);
case {'L','l'}
if Exp(expN).Dexp(DexpN).meanP(DMj,m)~=0
Rn(1)= Exp(expN).Dexp(DexpN).meanP(DN0,m);
Rs(1)= Exp(expN).Dexp(DexpN).stdP(DM0,m);
Rn(1)=Exp(expN).Dexp(DexpN).meanP(DN0,m);
Rs(1)=Exp(expN).Dexp(DexpN).stdP(DM0,m);
elseif Exp(expN).Dexp(DexpN).meanP(DMj,m)==0||isempty(Exp(expN).Dexp(DexpN).meanP(DMj,m)) &&...
strcmpi(ctrlRF,'G')
Rn(1)= Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstdG(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstdG(DM0);
end
end
pertRF= cell2mat(answer(anN(2)))
pertRF=cell2mat(answer(anN(2)))
switch pertRF
case {'G','g'}
Rn(2:dmN)= Exp(expN).Dexp(DexpN).RFmeanG(2:end);
Rs(2:dmN)= Exp(expN).Dexp(DexpN).RFstdG(2:end);
Rn(2:dmN)=Exp(expN).Dexp(DexpN).RFmeanG(2:end);
Rs(2:dmN)=Exp(expN).Dexp(DexpN).RFstdG(2:end);
case {'L','l'}
if Exp(expN).Dexp(DexpN).meanP(DMj,m)~=0
Rn(j)= Exp(expN).Dexp(DexpN).meanP(DMj,m);
Rs(j)= Exp(expN).Dexp(DexpN).stdP(DMj,m);
Rn(j)=Exp(expN).Dexp(DexpN).meanP(DMj,m);
Rs(j)=Exp(expN).Dexp(DexpN).stdP(DMj,m);
elseif Exp(expN).Dexp(DexpN).meanP(DMj,m)==0||isempty(Exp(expN).Dexp(DexpN).meanP(DMj,m)) &&...
strcmpi(ctrlRF,'G')
Rn(j)= Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)= Exp(expN).Dexp(DexpN).RFstdG(DMj);
Rn(j)=Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)=Exp(expN).Dexp(DexpN).RFstdG(DMj);
end
end
end
if RFconfig==3
ctrlRF= cell2mat(answer(anN(1)))
ctrlRF=cell2mat(answer(anN(1)))
switch ctrlRF
case {'F','f'}
Rn(1)= Exp(expN).Dexp(DexpN).RFmean(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstd(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmean(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstd(DM0);
case {'G','g'}
Rn(1)= Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstdG(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstdG(DM0);
case {'L','l'}
Rn(1)= Exp(expN).Dexp(DexpN).meanP(DM0,m);
Rs(1)= Exp(expN).Dexp(DexpN).stdP(DM0,m);
Rn(1)=Exp(expN).Dexp(DexpN).meanP(DM0,m);
Rs(1)=Exp(expN).Dexp(DexpN).stdP(DM0,m);
if Exp(expN).Dexp(DexpN).meanP(DMj,m)~=0,
Rn(1)= Exp(expN).Dexp(DexpN).meanP(DM0,m);
Rs(1)= Exp(expN).Dexp(DexpN).stdP(DM0,m);
Rn(1)=Exp(expN).Dexp(DexpN).meanP(DM0,m);
Rs(1)=Exp(expN).Dexp(DexpN).stdP(DM0,m);
elseif Exp(expN).Dexp(DexpN).meanP(DM0,m)==0 && strcmpi(ctrlRF,'G')
Rn(1)= Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstdG(DMj);
Rn(1)=Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstdG(DMj);
elseif Exp(expN).Dexp(DexpN).meanP(DM0,m)==0 && strcmpi(ctrlRF,'F')
Rn(1)= Exp(expN).Dexp(DexpN).RFmean(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstd(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmean(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstd(DM0);
elseif Exp(expN).Dexp(DexpN).meanP(DM0,m)==0 && strcmpi(ctrlRF,'L')
Rn(1)= Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)= Exp(expN).Dexp(DexpN).RFstdG(DM0);
Rn(1)=Exp(expN).Dexp(DexpN).RFmeanG(DM0);
Rs(1)=Exp(expN).Dexp(DexpN).RFstdG(DM0);
end
end
pertRF= cell2mat(answer(anN(2)))
pertRF=cell2mat(answer(anN(2)))
switch pertRF
case {'F','f'}
Rn(2:dmN)= Exp(expN).Dexp(DexpN).RFmean(2:end);
Rs(2:dmN)= Exp(expN).Dexp(DexpN).RFstd(2:end);
Rn(2:dmN)=Exp(expN).Dexp(DexpN).RFmean(2:end);
Rs(2:dmN)=Exp(expN).Dexp(DexpN).RFstd(2:end);
case {'G','g'}
Rn(2:dmN)= Exp(expN).Dexp(DexpN).RFmeanG(2:end);
Rs(2:dmN)= Exp(expN).Dexp(DexpN).RFstdG(2:end);
Rn(2:dmN)=Exp(expN).Dexp(DexpN).RFmeanG(2:end);
Rs(2:dmN)=Exp(expN).Dexp(DexpN).RFstdG(2:end);
case {'L','l'}
if Exp(expN).Dexp(DexpN).meanP(DMj,m)~=0,
Rn(j)= Exp(expN).Dexp(DexpN).meanP(DMj,m);
Rs(j)= Exp(expN).Dexp(DexpN).stdP(DMj,m);
Rn(j)=Exp(expN).Dexp(DexpN).meanP(DMj,m);
Rs(j)=Exp(expN).Dexp(DexpN).stdP(DMj,m);
elseif Exp(expN).Dexp(DexpN).meanP(DMj,m)==0 && strcmpi(ctrlRF,'G')
Rn(j)= Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)= Exp(expN).Dexp(DexpN).RFstdG(DMj);
Rn(j)=Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)=Exp(expN).Dexp(DexpN).RFstdG(DMj);
elseif Exp(expN).Dexp(DexpN).meanP(DMj,m)==0 && strcmpi(ctrlRF,'F')
Rn(j)= Exp(expN).Dexp(DexpN).RFmean(DMj);
Rs(j)= Exp(expN).Dexp(DexpN).RFstd(DMj);
Rn(j)=Exp(expN).Dexp(DexpN).RFmean(DMj);
Rs(j)=Exp(expN).Dexp(DexpN).RFstd(DMj);
elseif Exp(expN).Dexp(DexpN).meanP(DMj,m)==0 && strcmpi(ctrlRF,'L')
Rn(j)= Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)= Exp(expN).Dexp(DexpN).RFstdG(DMj);
Rn(j)=Exp(expN).Dexp(DexpN).RFmeanG(DMj);
Rs(j)=Exp(expN).Dexp(DexpN).RFstdG(DMj);
end
end
end

321
workflow/apps/matlab/ezview/EZlstBoxCmpExt.m
View File

@@ -3,194 +3,189 @@
%Provides Trace data storage for use by EZfigTrendOL.m
RFcmpGFlg=0;
if isequal(tempLB(4:6),'cmp'), RFnum= str2double(tempLB(3));
elseif isequal(tempLB(3:6),'cmpG'), RFcmpGFlg=1;
elseif isequal(tempLB(3:6),'cmpP'), RFcmpGFlg=1; %I beleive handling will be the same as RFcmpG
if isequal(tempLB(4:6),'cmp')
RFnum=str2double(tempLB(3));
elseif isequal(tempLB(3:6),'cmpG')
RFcmpGFlg=1;
elseif isequal(tempLB(3:6),'cmpP')
RFcmpGFlg=1; %I beleive handling will be the same as RFcmpG
end
Exp(expN).cLmdEven= 0; %Added for Cummulative Median and Mean 'C' plot
Exp(expN).cLmdEven=0; %Added for Cummulative Median and Mean 'C' plot
RFDMflg=0;
if zoneSel==1,DexpN= (get(ghandles.DN1,'value')); end
if zoneSel==2,DexpN= (get(ghandles.DN2,'value')); end
if zoneSel==3,DexpN= (get(ghandles.DN3,'value')); end
if zoneSel==1,DexpN=(get(ghandles.DN1,'value')); end
if zoneSel==2,DexpN=(get(ghandles.DN2,'value')); end
if zoneSel==3,DexpN=(get(ghandles.DN3,'value')); end
try
p1=cell2mat(strfind(selGnOrf,'('));
p2= cell2mat(strfind(selGnOrf,')'));
dmNum= str2num(selGnOrf{1}(p1+1:p2-1));
inDM= str2num(selGnOrf{1}(p1+1:p2-1));
if (~isempty(dmNum)&& isnumeric(dmNum)),RFDMflg=1; end
p1=cell2mat(strfind(selGnOrf,'('));
p2=cell2mat(strfind(selGnOrf,')'));
dmNum=str2num(selGnOrf{1}(p1+1:p2-1));
inDM=str2num(selGnOrf{1}(p1+1:p2-1));
if (~isempty(dmNum)&& isnumeric(dmNum)),RFDMflg=1; end
catch
end
if RFDMflg, Exp(zoneSel).Dexp(DexpN).pertSel=dmNum; end %pertSel=pert;
sgdInfoOnly=get(handles.InfoToggle,'value');
if sgdInfoOnly==1
EZviewInfoBox
else % Runs to end of EZlstBoxExt.m within this else condition
%***********PLOT Selected Gene/Orf Spot ******************************************
%try
if RFcmpGFlg==0
K= Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).med; Ks= num2str(K);
r= Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).med; rs= num2str(r);
l= Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).med; Ls= num2str(l);
Kl= K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku= K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl= r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru= r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast= l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow= l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
elseif RFcmpGFlg==1
K= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks= num2str(K);
r= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs= num2str(r);
l= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls= num2str(l);
Kl= K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Ku= K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
rl= r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
ru= r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
lfast= l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
lslow= l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
end
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
% Plot Selected Gene/Orf Spot
%try
if RFcmpGFlg==0
K=Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).med; Ks=num2str(K);
r=Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).med; rs=num2str(r);
l=Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).med; Ls=num2str(l);
Kl=K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku=K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl=r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru=r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast=l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow=l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
elseif RFcmpGFlg==1
K=Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks=num2str(K);
r=Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs=num2str(r);
l=Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls=num2str(l);
Kl=K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Ku=K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
rl=r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
ru=r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
lfast=l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
lslow=l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
end
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
t=1:200;
clear g;
t=1:200;
clear g;
%try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
%tser=(scan(1,plateNum).plate(1).t0Series(:));
%rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
%try
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
%tser=(scan(1,plateNum).plate(1).t0Series(:));
%rawData=scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
if zoneSel==1
plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
Exp(1).traceN=Exp(1).traceN+1;
traceN=Exp(1).traceN;
end
if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
if zoneSel==2
plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
Exp(2).traceN=Exp(2).traceN+1;
traceN=Exp(2).traceN;
end
if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
if zoneSel==3
plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
Exp(3).traceN=Exp(3).traceN+1;
traceN=Exp(3).traceN;
end
plot(plotAxes,t,g);hold (plotAxes,'on'); %plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y'); plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
if RFcmpGFlg==0
Exp(expN).lstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
Exp(expN).kstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Exp(expN).rstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
plot(plotAxes,t,g);hold (plotAxes,'on'); % plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y'); plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug)
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrLvals= {Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(dm).Lvals};
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrKvals= {Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(dm).Kvals};
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).Usrrvals= {Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(dm).rvals};
end
% Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
if RFcmpGFlg==0
Exp(expN).lstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
Exp(expN).kstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Exp(expN).rstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug)
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrLvals={Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(dm).Lvals};
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrKvals={Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(dm).Kvals};
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).Usrrvals={Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(dm).rvals};
end
Exp(expN).Trace(traceN).dmSel=inDM;
Exp(expN).Trace(traceN).DexpN=DexpN;
Exp(expN).Trace(traceN).UsrGLB=selGnOrf;
elseif RFcmpGFlg==1
Exp(expN).lstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
Exp(expN).kstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Exp(expN).rstd(traceN)=Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
if strcmp(Exp(expN).DexpType,'chrono')
for nn=1:length(Exp(expN).Dexp) %replaced dmSel with inDM for 'chrono' and RFcmpGFlg
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).UsrLvals=Exp(expN).Dexp(nn).RFcmpGL.dm(inDM).Lvals;
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).UsrKvals=Exp(expN).Dexp(nn).RFcmpGK.dm(inDM).Kvals;
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).Usrrvals=Exp(expN).Dexp(nn).RFcmpGr.dm(inDM).rvals;
end
else
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug)
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrLvals=Exp(expN).Dexp(DexpN).RFcmpGL.dm(dm).Lvals;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrKvals=Exp(expN).Dexp(DexpN).RFcmpGK.dm(dm).Kvals;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).Usrrvals=Exp(expN).Dexp(DexpN).RFcmpGr.dm(dm).rvals;
end
end
Exp(expN).Trace(traceN).dmSel=inDM;
Exp(expN).Trace(traceN).DexpN=DexpN;
Exp(expN).Trace(traceN).UsrGLB=selGnOrf;
end
Exp(expN).Trace(traceN).dmSel= inDM;
Exp(expN).Trace(traceN).DexpN= DexpN;
Exp(expN).Trace(traceN).UsrGLB= selGnOrf;
Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;
Exp(expN).lKl(traceN)=Kl; Exp(expN).Ku(traceN)=Ku;
Exp(expN).lrl(traceN)=rl; Exp(expN).ru(traceN)=ru;
elseif RFcmpGFlg==1
Exp(expN).lstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
Exp(expN).kstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Exp(expN).rstd(traceN)= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
if strcmp(Exp(expN).DexpType,'chrono')
for nn=1:length(Exp(expN).Dexp) %replaced dmSel with inDM for 'chrono' and RFcmpGFlg
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).UsrLvals= Exp(expN).Dexp(nn).RFcmpGL.dm(inDM).Lvals;
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).UsrKvals= Exp(expN).Dexp(nn).RFcmpGK.dm(inDM).Kvals;
Exp(expN).Trace(traceN).Dexp(nn).DM(inDM).Usrrvals= Exp(expN).Dexp(nn).RFcmpGr.dm(inDM).rvals;
end
else
for dm=1:length(Exp(expN).Dexp(DexpN).DM.drug)
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrLvals= Exp(expN).Dexp(DexpN).RFcmpGL.dm(dm).Lvals;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).UsrKvals= Exp(expN).Dexp(DexpN).RFcmpGK.dm(dm).Kvals;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(dm).Usrrvals= Exp(expN).Dexp(DexpN).RFcmpGr.dm(dm).rvals;
end
end
Exp(expN).Trace(traceN).dmSel= inDM;
Exp(expN).Trace(traceN).DexpN= DexpN;
Exp(expN).Trace(traceN).UsrGLB= selGnOrf;
end
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
Exp(expN).lKl(traceN)= Kl; Exp(expN).Ku(traceN)= Ku;
Exp(expN).lrl(traceN)= rl; Exp(expN).ru(traceN)= ru;
%************************************************************************
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
%Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*'); %No Raw Data, Ref Composite 17_1009
%catch
try
for i=1:length(Exp(zoneSel).hOL(:))
set(Exp(zoneSel).hOL(i),'color',[0 0 1]);
end
catch
end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
% Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*'); %No Raw Data, Ref Composite 17_1009
% catch
% catchissue='Ln68 EZlstBoxCmpExt'
%end %trycatch
% end %trycatch
%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
% Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
if isequal(selGnOrf{1}(1:3),'RF1')|| isequal(selGnOrf{1}(1:3),'RF2')|| RFcmpGFlg==1
gene= {selGnOrf{1}(1:p2)};
geneOrfstr= gene;
grfgenestr= gene;
else
if isequal(selGnOrf{1}(1:3),'RF1')|| isequal(selGnOrf{1}(1:3),'RF2')|| RFcmpGFlg==1
gene={selGnOrf{1}(1:p2)};
geneOrfstr=gene;
grfgenestr=gene;
else
gene=MP(1,LBmp).genename{1,1}(indx); orf=MP(1,LBmp).orf{1,1}(indx);
geneOrfstr= strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr= strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
end
%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
geneOrfstr=strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr=strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
end
%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
end
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1;
expStr= {xp(startPos:endPos)}
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1;
expStr={xp(startPos:endPos)}
Exp(zoneSel).hOLname(traceN)= spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
%Exp(zoneSel).hOLplateNum(traceN)= plateNum;
Exp(zoneSel).hOLname(traceN)=spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)=graphStr;
Exp(zoneSel).hOLexpNm(traceN)=expStr; %ghandles.Exp(expN).hOLexpNm(traceN)=expStr;
Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
%Exp(zoneSel).hOLplateNum(traceN)=plateNum;
%traceData=vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
%catch
%catchissue='Ln33 EZlstBoxCmpExt'
% msg='Error'
%end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
%**************Write Spot and Exp Info to OLay title areas****************************************************************************
% Write Spot and Exp Info to OLay title areas
if zoneSel==1, %&& get(ghandles.rotPB1,'value')~=1
if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay1,'FontSize',8);end
@@ -210,29 +205,13 @@ if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);en
if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp3,'FontSize',8);end
set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(traceN));
end
end %if sgdInfoOnly==1
%***********************GraphicDestinationPerturbationComparison**15_0821************************************************
lstBoxCmpFlg=1;
EZdatatip=0; %**
if strcmp((Exp(expN).DexpType),'single')||...
strcmp((Exp(expN).DexpType),'multi')
%****************
EZdestComp %**
%****************
elseif strcmp((Exp(expN).DexpType),'chrono')
%EZdatatip=2; %**
%************
EZmDayTrend %**
%************
end
%***********************************************************************************************************************
% GraphicDestinationPerturbationComparison**15_0821
lstBoxCmpFlg=1;
EZdatatip=0;
if strcmp((Exp(expN).DexpType),'single') || strcmp((Exp(expN).DexpType),'multi')
EZdestComp
elseif strcmp((Exp(expN).DexpType),'chrono')
EZmDayTrend
end

432
workflow/apps/matlab/ezview/EZlstBoxExt.m
View File

@@ -1,160 +1,143 @@
%EZlstBoxExt.m
%Calls either EZdestComp.m
%or if 'Chrono' EZmDayPlotUCmp.m and EZmDayTrend.m and if ghandles.CompositeTog_,EZmDayPlotUcomposite
%or by EZviewGui.m (listboxGnOrf_Callback)
% Calls either EZdestComp.m
% or if 'Chrono' EZmDayPlotUCmp.m and EZmDayTrend.m and if ghandles.CompositeTog_,EZmDayPlotUcomposite
% or by EZviewGui.m (listboxGnOrf_Callback)
%Replace get(ghandles.CompositeTog1,'value')==1 ... with get(handles....
if expN==1 && get(handles.CompositeTog1,'value')==1 ||...
expN==2 && get(handles.CompositeTog2,'value')==1 ||...
expN==3 && get(handles.CompositeTog3,'value')==1
% Replace get(ghandles.CompositeTog1,'value')==1 ... with get(handles....
if expN==1 && get(handles.CompositeTog1,'value')==1 ...
|| expN==2 && get(handles.CompositeTog2,'value')==1 ...
|| expN==3 && get(handles.CompositeTog3,'value')==1
CompositeTrendFlg=1; else CompositeTrendFlg=0;
end
Exp(expN).cLmdEven= 0; %Added for Cummulative Median and Mean 'C' plot
Exp(expN).cLmdEven=0; % Added for Cummulative Median and Mean 'C' plot
RFDMflg=0;
if zoneSel==1,DexpN= (get(handles.DN1,'value')); end
if zoneSel==2,DexpN= (get(handles.DN2,'value')); end
if zoneSel==3,DexpN= (get(handles.DN3,'value')); end
if zoneSel==1,DexpN=(get(handles.DN1,'value')); end
if zoneSel==2,DexpN=(get(handles.DN2,'value')); end
if zoneSel==3,DexpN=(get(handles.DN3,'value')); end
try
p1=cell2mat(strfind(selGnOrf,'('));
p2= cell2mat(strfind(selGnOrf,')'));
dmNum= str2num(selGnOrf{1}(p1+1:p2-1));
inDM= selGnOrf{1}(p1+1:p2-1);
if (~isempty(dmNum)&& isnumeric(dmNum)),RFDMflg=1; end
p1=cell2mat(strfind(selGnOrf,'('));
p2=cell2mat(strfind(selGnOrf,')'));
dmNum=str2num(selGnOrf{1}(p1+1:p2-1));
inDM=selGnOrf{1}(p1+1:p2-1);
if (~isempty(dmNum)&& isnumeric(dmNum)),RFDMflg=1; end
catch
end
if RFDMflg, Exp(zoneSel).Dexp(DexpN).pertSel=dmNum; end %pertSel=pert;
if RFDMflg, Exp(zoneSel).Dexp(DexpN).pertSel=dmNum; end % pertSel=pert;
inMP=selGnOrf{1}((LBdlims{:,:}(1))+1:(LBdlims{:,:}(2))-1)
%LBmp=str2double(inMP);
% LBmp=str2double(inMP);
sgdInfoOnly=get(handles.InfoToggle,'value');
if sgdInfoOnly==1
%***************
EZviewInfoBox %*
%***************
EZviewInfoBox
else % Runs to end of EZlstBoxExt.m within this else condition
if zoneSel==1
Max=floor(get(handles.MPsldr1,'max'));
Min=floor(get(handles.MPsldr1,'min'));
if str2num(inMP) >= Min && str2num(inMP) <= Max
set(handles.MPed1,'string',inMP)
set(handles.MPsldr1,'value',str2double(inMP));
else
if str2num(inMP) >= Max, set(handles.MPsldr1,'value',Max); set(handles.MPed1,'string',num2str(Max));end
if str2num(inMP) <= Min, set(handles.MPsldr1,'value',Min),set(handles.MPed1,'string',num2str(Min));end
end
end
if zoneSel==2
Max=floor(get(handles.MPsldr2,'max'));
Min=floor(get(handles.MPsldr2,'min'));
if str2num(inMP) >= Min && str2num(inMP) <= Max
set(handles.MPed2,'string',inMP)
set(handles.MPsldr2,'value',str2double(inMP));
else
if str2num(inMP) >= Max, set(handles.MPsldr2,'value',Max); set(handles.MPed2,'string',num2str(Max));end
if str2num(inMP) <= Min, set(handles.MPsldr2,'value',Min),set(handles.MPed2,'string',num2str(Min));end
end
end
if zoneSel==3
Max=floor(get(handles.MPsldr3,'max'));
Min=floor(get(handles.MPsldr3,'min'));
if str2num(inMP) >= Min && str2num(inMP) <= Max
set(handles.MPed3,'string',inMP)
set(handles.MPsldr3,'value',str2double(inMP));
else
if str2num(inMP) >= Max, set(handles.MPsldr3,'value',Max); set(handles.MPed3,'string',num2str(Max));end
if str2num(inMP) <= Min, set(handles.MPsldr3,'value',Min),set(handles.MPed3,'string',num2str(Min));end
end
end
if zoneSel==1
Max=floor(get(handles.MPsldr1,'max'));
Min=floor(get(handles.MPsldr1,'min'));
if str2num(inMP) >=Min && str2num(inMP) <=Max
set(handles.MPed1,'string',inMP)
set(handles.MPsldr1,'value',str2double(inMP));
else
if str2num(inMP) >=Max, set(handles.MPsldr1,'value',Max); set(handles.MPed1,'string',num2str(Max));end
if str2num(inMP) <=Min, set(handles.MPsldr1,'value',Min),set(handles.MPed1,'string',num2str(Min));end
end
end
if zoneSel==2
Max=floor(get(handles.MPsldr2,'max'));
Min=floor(get(handles.MPsldr2,'min'));
if str2num(inMP) >=Min && str2num(inMP) <=Max
set(handles.MPed2,'string',inMP)
set(handles.MPsldr2,'value',str2double(inMP));
else
if str2num(inMP) >=Max, set(handles.MPsldr2,'value',Max); set(handles.MPed2,'string',num2str(Max));end
if str2num(inMP) <=Min, set(handles.MPsldr2,'value',Min),set(handles.MPed2,'string',num2str(Min));end
end
end
if zoneSel==3
Max=floor(get(handles.MPsldr3,'max'));
Min=floor(get(handles.MPsldr3,'min'));
if str2num(inMP) >=Min && str2num(inMP) <=Max
set(handles.MPed3,'string',inMP)
set(handles.MPsldr3,'value',str2double(inMP));
else
if str2num(inMP) >=Max, set(handles.MPsldr3,'value',Max); set(handles.MPed3,'string',num2str(Max));end
if str2num(inMP) <=Min, set(handles.MPsldr3,'value',Min),set(handles.MPed3,'string',num2str(Min));end
end
end
if RFDMflg
if zoneSel==1
Max=floor(get(handles.DMsldr1,'max'));
Min=floor(get(handles.DMsldr1,'min'));
if str2num(inDM) >=Min && str2num(inDM) <=Max
set(handles.DMed1,'string',inDM)
set(handles.DMsldr1,'value',str2double(inDM));
else
if str2num(inDM) >=Max, set(handles.DMsldr1,'value',Max); set(handles.DMed1,'string',num2str(Max));end
if str2num(inDM) <=Min, set(handles.DMsldr1,'value',Min),set(handles.DMed1,'string',num2str(Min));end
end
end
if zoneSel==2
Max=floor(get(handles.DMsldr2,'max'));
Min=floor(get(handles.DMsldr2,'min'));
if str2num(inDM) >=Min && str2num(inDM) <=Max
set(handles.DMed2,'string',inDM)
set(handles.DMsldr2,'value',str2double(inDM));
else
if str2num(inDM) >=Max, set(handles.DMsldr2,'value',Max); set(handles.DMed2,'string',num2str(Max));end
if str2num(inDM) <=Min, set(handles.DMsldr2,'value',Min),set(handles.DMed2,'string',num2str(Min));end
end
end
if zoneSel==3
Max=floor(get(handles.DMsldr3,'max'));
Min=floor(get(handles.DMsldr3,'min'));
if str2num(inDM) >=Min && str2num(inDM) <=Max
set(handles.DMed3,'string',inDM)
set(handles.DMsldr3,'value',str2double(inDM));
else
if str2num(inDM) >=Max, set(handles.DMsldr3,'value',Max); set(handles.DMed3,'string',num2str(Max));end
if str2num(inDM) <=Min, set(handles.DMsldr3,'value',Min),set(handles.DMed3,'string',num2str(Min));end
end
end
end
if RFDMflg,
if zoneSel==1
Max=floor(get(handles.DMsldr1,'max'));
Min=floor(get(handles.DMsldr1,'min'));
if str2num(inDM) >= Min && str2num(inDM) <= Max
set(handles.DMed1,'string',inDM)
set(handles.DMsldr1,'value',str2double(inDM));
else
if str2num(inDM) >= Max, set(handles.DMsldr1,'value',Max); set(handles.DMed1,'string',num2str(Max));end
if str2num(inDM) <= Min, set(handles.DMsldr1,'value',Min),set(handles.DMed1,'string',num2str(Min));end
end
end
if zoneSel==2
Max=floor(get(handles.DMsldr2,'max'));
Min=floor(get(handles.DMsldr2,'min'));
if str2num(inDM) >= Min && str2num(inDM) <= Max
set(handles.DMed2,'string',inDM)
set(handles.DMsldr2,'value',str2double(inDM));
else
if str2num(inDM) >= Max, set(handles.DMsldr2,'value',Max); set(handles.DMed2,'string',num2str(Max));end
if str2num(inDM) <= Min, set(handles.DMsldr2,'value',Min),set(handles.DMed2,'string',num2str(Min));end
end
end
if zoneSel==3
Max=floor(get(handles.DMsldr3,'max'));
Min=floor(get(handles.DMsldr3,'min'));
if str2num(inDM) >= Min && str2num(inDM) <= Max
set(handles.DMed3,'string',inDM)
set(handles.DMsldr3,'value',str2double(inDM));
else
if str2num(inDM) >= Max, set(handles.DMsldr3,'value',Max); set(handles.DMed3,'string',num2str(Max));end
if str2num(inDM) <= Min, set(handles.DMsldr3,'value',Min),set(handles.DMed3,'string',num2str(Min));end
end
end
end
%**************************************************************************
EZVimDisplay %**
%**************************************************************************
%17_111 If CompositeTog_ set, Routine called to find all gene replicates and produce composite values
if CompositeTrendFlg==1
if strcmp(Exp(expN).DexpType, 'chrono')
%***********************
EZmDayPlotUcmp %*
%***********************
else
%***********************
EZplotUcmp %*
%***********************
end
EZVimDisplay
%*******************************************************************
%***********PLOT Selected Gene/Orf Spot ******************************************
% if non-Composite ("normal") then - ...
elseif CompositeTrendFlg~=1
destPerMP= Exp(zoneSel).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
% 17_111 If CompositeTog_ set, Routine called to find all gene replicates and produce composite values
if CompositeTrendFlg==1
if strcmp(Exp(expN).DexpType, 'chrono')
EZmDayPlotUcmp
else
EZplotUcmp
end
% Plot Selected Gene/Orf Spot
% if non-Composite ("normal") then - ...
elseif CompositeTrendFlg~=1
destPerMP=Exp(zoneSel).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
indx=((LBr-1)*24) +LBc
MP=Exp(zoneSel).Dexp(DexpN).MP;
try
K=scan(1,plateNum).plate(1).CFout(indx,3); Ks= num2str(K);
r=scan(1,plateNum).plate(1).CFout(indx,4); rs= num2str(r);
l=scan(1,plateNum).plate(1).CFout(indx,5); Ls= num2str(l);
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
Kl=scan(1,plateNum).plate(1).CFout(indx,7);
Ku=scan(1,plateNum).plate(1).CFout(indx,8);
rl=scan(1,plateNum).plate(1).CFout(indx,9);
ru=scan(1,plateNum).plate(1).CFout(indx,10);
lfast=scan(1,plateNum).plate(1).CFout(indx,11);
lslow=scan(1,plateNum).plate(1).CFout(indx,12);
t=1:200;
clear g;
try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
tser=(scan(1,plateNum).plate(1).t0Series(:));
rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
try
K=scan(1,plateNum).plate(1).CFout(indx,3); Ks=num2str(K);
r=scan(1,plateNum).plate(1).CFout(indx,4); rs=num2str(r);
l=scan(1,plateNum).plate(1).CFout(indx,5); Ls=num2str(l);
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
Kl=scan(1,plateNum).plate(1).CFout(indx,7);
Ku=scan(1,plateNum).plate(1).CFout(indx,8);
rl=scan(1,plateNum).plate(1).CFout(indx,9);
ru=scan(1,plateNum).plate(1).CFout(indx,10);
lfast=scan(1,plateNum).plate(1).CFout(indx,11);
lslow=scan(1,plateNum).plate(1).CFout(indx,12);
t=1:200;
clear g;
try
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
tser=(scan(1,plateNum).plate(1).t0Series(:));
rawData=scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
Exp(1).traceN=Exp(1).traceN+1;
@@ -170,75 +153,69 @@ rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(i
Exp(3).traceN=Exp(3).traceN+1;
traceN=Exp(3).traceN;
end
plot(plotAxes,t,g);hold (plotAxes,'on');plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
%************************************************************************
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*');
catch
plot(plotAxes,t,g);hold (plotAxes,'on');plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
% Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*');
catch
catchissue='Ln100 EZlstBoxExt'
end %trycatch
end
%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
% Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
if isequal(selGnOrf{1}(1:3),'RF1')
gene= {selGnOrf{1}(1:p2)};
geneOrfstr= strcat(gene,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr= strcat(gene,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
else
if isequal(selGnOrf{1}(1:3),'RF1')
gene={selGnOrf{1}(1:p2)};
geneOrfstr=strcat(gene,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr=strcat(gene,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
else
gene=MP(1,LBmp).genename{1,1}(indx); orf=MP(1,LBmp).orf{1,1}(indx);
geneOrfstr= strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr= strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
end
spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
geneOrfstr=strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc),'_',tPtStr);
grfgenestr=strcat(gene,'_',orf,'_','m',num2str(LBmp),'r',num2str(LBr),'c',num2str(LBc));
end
spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
end
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr= {xp(startPos:endPos)}
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr={xp(startPos:endPos)}
Exp(zoneSel).hOLname(traceN)= spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)= plateNum;
Exp(zoneSel).hOLname(traceN)=spotDescrip; % graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)=graphStr;
Exp(zoneSel).hOLexpNm(traceN)=expStr; % ghandles.Exp(expN).hOLexpNm(traceN)=expStr;
Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)=plateNum;
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
catch
% traceData=vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
catch
catchissue='Ln141 EZlstBoxExt'
msg='Error'
end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
end
end
end %if get(ghandles.CompositeTog1,'value')==1
%**************Write Spot and Exp Info to OLay title areas****************************************************************************
if zoneSel==1, %&& get(ghandles.rotPB1,'value')~=1
% Write Spot and Exp Info to OLay title areas
if zoneSel==1 %&& get(ghandles.rotPB1,'value')~=1
if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay1,'FontSize',8);end
set(ghandles.OLay1,'string', Exp(zoneSel).hOLname(traceN));
if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp1,'FontSize',8);end
@@ -257,51 +234,44 @@ end %if get(ghandles.CompositeTog1,'value')==1
set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(traceN));
end
%*****************Highlight gene/orf select Spot on Image*********
tPtSel=Exp(zoneSel).Dexp(DexpN).tPtSel;
Rim= 16-(LBr-1); Cim =LBc;
spotCoor=Exp(zoneSel).Dexp(DexpN).FexpScanSpots{1,plateNum}{Cim,Rim,tPtSel};
% Highlight gene/orf select Spot on Image
tPtSel=Exp(zoneSel).Dexp(DexpN).tPtSel;
Rim=16-(LBr-1); Cim =LBc;
spotCoor=Exp(zoneSel).Dexp(DexpN).FexpScanSpots{1,plateNum}{Cim,Rim,tPtSel};
if zoneSel==1, expAxes=ghandles.Iaxes1;end
if zoneSel==2, expAxes=ghandles.Iaxes2;end
if zoneSel==3, expAxes=ghandles.Iaxes3;end
%axes(ghandles.Iaxes1)
plot(expAxes,(spotCoor(2)+24),(spotCoor(1)+24),'.y')
% GraphicDestinationPerturbationComparison**15_0821
EZdatatip=0; %**
if strcmp((Exp(expN).DexpType),'single') ...
|| strcmp((Exp(expN).DexpType),'multi')
EZdestComp
elseif strcmp((Exp(expN).DexpType),'chrono')
EZmDayTrend
end
%***********************GraphicDestinationPerturbationComparison**15_0821************************************************
EZdatatip=0; %**
if strcmp((Exp(expN).DexpType),'single')||...
strcmp((Exp(expN).DexpType),'multi')
%****************
EZdestComp %**
%****************
elseif strcmp((Exp(expN).DexpType),'chrono')
%************
EZmDayTrend %**
%************
end
%***********************************************************************************************************************
%*********************HeatMap Text Field*********************************
try
ll=num2str(l);
if length(ll)>5,htl= ll(1:5);else htl=ll;end
catch
% HeatMap Text Field
try
ll=num2str(l);
if length(ll)>5,htl=ll(1:5);else htl=ll;end
catch
htl=' ';
end
try
n1= num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1= n1(1:5);else N1=n1; end
end
try
n1=num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1=n1(1:5);else N1=n1; end
htN1=strcat('_N1=',N1);
catch,
catch,
htN1=' ';
end
try
htmapStr=strcat('L=',htl, htN1)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
catch
end
end
try
htmapStr=strcat('L= ',htl, htN1)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
catch
end
end %if sgdInfoOnly==1

369
workflow/apps/matlab/ezview/EZmDayPlotUcmp.m
View File

@@ -1,153 +1,127 @@
%***********User find and build composite of Selected Gene Composite and
%*************Plot it on OLay Plot and Trend plot DNLaxles
%***************For Chonological Studies (multi Day Studies)
%Called when Composite_ toggle button is clicked.
%Data stored for printable Trend Plot production (click [L] in DNLaxes )
%*********************
% User find and build composite of Selected Gene Composite and
% Plot it on OLay Plot and Trend plot DNLaxles
% For Chonological Studies (multi Day Studies)
% Called when Composite_ toggle button is clicked.
% Data stored for printable Trend Plot production (click [L] in DNLaxes )
global ghandles
global Exp
global exDlst
global exFolder
traceN=Exp(expN).traceN;
DexpN= Exp(expN).DexpN; %Temp input for development
DexpN=Exp(expN).DexpN; % Temp input for development
patrnN=strfind(selGnOrf{1},':'); %Extract Gene-Orf Name
patrndash= strfind(selGnOrf{1},'-');
selStrNm= char(selGnOrf)
patrndash=strfind(selGnOrf{1},'-');
selStrNm=char(selGnOrf)
if strcmpi(selStrNm(1:3),'RF-')
usrGene= selStrNm(4:(patrndash(2)-1));
usrGene=selStrNm(4:(patrndash(2)-1));
else
usrGene= selStrNm(1:(patrnN(1)-1));
usrGene=selStrNm(1:(patrnN(1)-1));
end
prompt={'Enter Specifics Term if used to futher specify selection '}
dlg_title='User Specifics Term for Refinement Composite';
num_lines=1;
def={'None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
usrSpec=cell2mat(answer(1));
if strcmpi(usrSpec,'None')
usrGnSp={strcat(usrGene,'-')};
elseif length(usrSpec)> 8,
trimUspec=usrSpec(1:8);
usrGnSp=strcat(usrGene,',',{trimUspec});
else
trimUspec=usrSpec;
usrGnSp=strcat(usrGene,',',{trimUspec});
end
prompt={'Enter Specifics Term if used to futher specify selection '}
dlg_title='User Specifics Term for Refinement Composite';
num_lines=1;
def={'None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
usrSpec= cell2mat(answer(1));
if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')};
elseif length(usrSpec)> 8,
trimUspec= usrSpec(1:8);
usrGnSp= strcat(usrGene,',',{trimUspec});
else
trimUspec= usrSpec;
usrGnSp= strcat(usrGene,',',{trimUspec});
end
for n=1:Exp(expN).DexpLength % LOOP Thru DayExps
MPnum=length(Exp(expN).Dexp(n).MP);
DMnum=length(Exp(expN).Dexp(n).DM.drug);
%Extract expDay from ExpName string
dayNpos=max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'))
dayLbl=Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);
dRF1indx=0;
usrSp=usrSpec; %user entry of Specifics for Ref selection
for n=1:Exp(expN).DexpLength %LOOP Thru DayExps
MPnum=length(Exp(expN).Dexp(n).MP);
DMnum= length(Exp(expN).Dexp(n).DM.drug);
%Extract expDay from ExpName string
dayNpos= max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'))
dayLbl= Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);
%*********************************
dRF1indx=0;
usrSp= usrSpec; %user entry of Specifics for Ref selection
%*******************************************************
for mp=1:length(Exp(expN).Dexp(n).MP)
for mp=1:length(Exp(expN).Dexp(n).MP)
for ind384=1:384
try %
%Insert test for numeric in genename and orf if isnumeric
%Correct common EXCEL problem of converting OCT1 into a date numeric
try
% Insert test for numeric in genename and orf if isnumeric
% Correct common EXCEL problem of converting OCT1 into a date numeric
if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991,
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'};
elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '};
end
%*****************************************************************
%DISPersed REFerence capture and find Medians
if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp)))...
|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
strcmpi(usrSp,'None'))) ),
% DISPersed REFerence capture and find Medians
if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ...
&& strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp))) ...
|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ...
&& strcmpi(usrSp,'None'))) )
dRF1indx=dRF1indx+1;
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)= (Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)= mp;
drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)= ind384;
%drf(dRF1indx,7)= (Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
end %if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...
%*******************************************************************************
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)=(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)=mp;
drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)=ind384;
%drf(dRF1indx,7)=(Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
end
catch
msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
end
end % end associated with for ind384=1:384
mp
end
end %end associated with for ind384=1:384
mp
end %end associated with for mp=1:length(Exp(expN).Dexp(n).MP)
%*****************************************************
%************************************************************************************************
vvL=[]; %Initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
if exist('drf','var')
%Det. index of change from one MP to the next
vvL=[]; %Initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
if exist('drf','var')
% Det. index of change from one MP to the next
i=2;
clear chgIndx
chgIndx(1)=1;
for j=1:length(drf(:,3))
for j=1:length(drf(:,3))
if j>1
if cell2mat(drf(j,2))~= cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end
if cell2mat(drf(j,2))~=cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end
end
end
chgIndx(length(chgIndx)+1)= size(drf,1) +1; %length(drf)+1;
vvL= zeros(size(drf,1),1 ); %length(drf)+1;
%************************************
dMPs= unique(cell2mat(drf(:,2)));
%*****************************************
end
chgIndx(length(chgIndx)+1)=size(drf,1) +1; %length(drf)+1;
vvL=zeros(size(drf,1),1 ); %length(drf)+1;
dMPs=unique(cell2mat(drf(:,2)));
for mm=1:length(dMPs) % length(chgIndx)
usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel);
NZusrIndx= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp= NZusrIndx;
NZusrIndx=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp=NZusrIndx;
vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5);
%For Global Ref Composite 17_1009 %**************************************************************************
% For Global Ref Composite 17_1009
vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4);
%*****************************************************************************************************
end %for mm=1:length(dMPs)
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
for d=dmSel:dmSel
NZusrIndxG=[];
NZusrIndxG= find(vvL);
if isempty(nonzeros(vvL)), nonZeroCntD=0;
else nonZeroCntD= length(nonzeros(vvL));
end
%Calc. of median value for composite doesn't require and odd number of Indx items
NZusrIndxG= NZusrIndxG(:);
if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
UsrLvals{n}= vvL(NZusrIndxG);
UsrKvals{n}= vvK(NZusrIndxG);
Usrrvals{n}= vvr(NZusrIndxG);
% Calc. Global Mean, Std, And Median For Distributed References
for d=dmSel:dmSel
NZusrIndxG=[];
NZusrIndxG=find(vvL);
if isempty(nonzeros(vvL))
nonZeroCntD=0;
else
nonZeroCntD=length(nonzeros(vvL));
end
% Calc. of median value for composite doesn't require and odd number of Indx items
NZusrIndxG=NZusrIndxG(:);
if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
UsrLvals{n}=vvL(NZusrIndxG);
UsrKvals{n}=vvK(NZusrIndxG);
Usrrvals{n}=vvr(NZusrIndxG);
end
end
end
end
end % if exist('drf','var')
%END OF DISPERSE Gene data collection
%*********************************************************************
%####################################################################
end %for n=1:Exp(expN).DexpLength %Loop thru Dayexps
if ~exist('drf','var'),
errordlg('Gene-Specifics combination not found. Check spelling of Specifics entry.','Entry Warning');
break;
@@ -159,134 +133,119 @@ if isempty(vvL),
NoGrowthflg=1;
end
%Exp(expN).UgeneCnt= Exp(expN).UgeneCnt +1;
%Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)= usrGnSp;
%#######################################################################
%***********PLOT Values Selected Gene-Specifics Composite ******************************************try
%Exp(expN).UgeneCnt=Exp(expN).UgeneCnt +1;
%Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)=usrGnSp;
% Plot Values Selected Gene-Specifics Composite
if NoGrowthflg==0
smpSz= size(NZusrIndxG,1);
K= median(cell2mat((UsrKvals(DexpN)))); Ks= num2str(K); Kstd= std(cell2mat((UsrKvals(DexpN)))); KstdStr= num2str(Kstd);
r= median(cell2mat((Usrrvals(DexpN)))); rs= num2str(r); rstd= std(cell2mat((Usrrvals(DexpN)))); rstdStr= num2str(rstd);
l= median(cell2mat((UsrLvals(DexpN)))); Ls= num2str(l); Lstd= std(cell2mat((UsrLvals(DexpN)))); LstdStr= num2str(Lstd);
Kl= K - Kstd; %std(UsrKvals(DexpN));
Ku= K + Kstd; %std(UsrKvals(DexpN));
rl= r - rstd; %std(Usrrvals(DexpN));
ru= r + rstd; %std(UsrKvals(DexpN));
lfast= l - Lstd;
lslow= l + Lstd;
smpSz=size(NZusrIndxG,1);
K=median(cell2mat((UsrKvals(DexpN)))); Ks=num2str(K); Kstd=std(cell2mat((UsrKvals(DexpN)))); KstdStr=num2str(Kstd);
r=median(cell2mat((Usrrvals(DexpN)))); rs=num2str(r); rstd=std(cell2mat((Usrrvals(DexpN)))); rstdStr=num2str(rstd);
l=median(cell2mat((UsrLvals(DexpN)))); Ls=num2str(l); Lstd=std(cell2mat((UsrLvals(DexpN)))); LstdStr=num2str(Lstd);
Kl=K - Kstd; %std(UsrKvals(DexpN));
Ku=K + Kstd; %std(UsrKvals(DexpN));
rl=r - rstd; %std(Usrrvals(DexpN));
ru=r + rstd; %std(UsrKvals(DexpN));
lfast=l - Lstd;
lslow=l + Lstd;
elseif NoGrowth==1 %if all data is zero (NoGrowth)
smpSz= size(NZusrIndxG,1);
K= 0; Ks= num2str(K); Kstd= 0; KstdStr= num2str(0);
r= 0; rs= num2str(r); rstd= 0; rstdStr= num2str(0);
l= 0; Ls= num2str(l); Lstd= 0; LstdStr= num2str(0);
Kl= K - Kstd;
Ku= K + Kstd;
rl= r - rstd;
ru= r + rstd;
lfast= l - Lstd;
lslow= l + Lstd;
smpSz=size(NZusrIndxG,1);
K=0; Ks=num2str(K); Kstd=0; KstdStr=num2str(0);
r=0; rs=num2str(r); rstd=0; rstdStr=num2str(0);
l=0; Ls=num2str(l); Lstd=0; LstdStr=num2str(0);
Kl=K - Kstd;
Ku=K + Kstd;
rl=r - rstd;
ru=r + rstd;
lfast=l - Lstd;
lslow=l + Lstd;
end
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
MP=Exp(zoneSel).Dexp(DexpN).MP;
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
MP=Exp(zoneSel).Dexp(DexpN).MP;
try
t=1:200;
clear g;
try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
t=1:200;
clear g;
try
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
Exp(1).traceN=Exp(1).traceN+1;
traceN=Exp(1).traceN;
end
if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
if zoneSel==2
plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
Exp(2).traceN=Exp(2).traceN+1;
traceN=Exp(2).traceN;
end
if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
if zoneSel==3
plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
Exp(3).traceN=Exp(3).traceN+1;
traceN=Exp(3).traceN;
end
plot(plotAxes,t,g);hold (plotAxes,'on');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
plot(plotAxes,t,g);hold (plotAxes,'on');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
Exp(expN).Trace(traceN).UsrGLB=usrGnSp;
Exp(expN).Trace(traceN).dmSel=dmSel;
for n=1:Exp(expN).DexpLength % Loop Thru DayExps
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrLvals=UsrLvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrKvals=UsrKvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).Usrrvals=Usrrvals(n);
end
Exp(expN).Trace(traceN).UsrGLB= usrGnSp;
Exp(expN).Trace(traceN).dmSel= dmSel;
for n=1:Exp(expN).DexpLength %LOOP Thru DayExps
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrLvals= UsrLvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrKvals= UsrKvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).Usrrvals= Usrrvals(n);
end
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for manual selected Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
%************************************************************************
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
% Store L R and K valves for manual selected Composite [C] plots
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;
catch
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
catch
catchissue='Ln100 EZlstBoxExt'
end %trycatch
end
%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
gene=usrGnSp; orf='' %MP(1,LBmp).orf{1,1}(indx);
geneOrfstr=strcat(gene,'_',orf,'_');
grfgenestr=strcat(gene,'_',orf,'_');
graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
spotDescrip=strcat(graphStr,'->',DMstr);
gene= usrGnSp; orf= '' %MP(1,LBmp).orf{1,1}(indx);
geneOrfstr= strcat(gene,'_',orf,'_');
grfgenestr= strcat(gene,'_',orf,'_');
graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
end
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1;
expStr= {xp(startPos:endPos)};
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1;
expStr={xp(startPos:endPos)};
Exp(zoneSel).hOLname(traceN)= spotDescrip;
Exp(zoneSel).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)= plateNum;
Exp(zoneSel).hOLname(traceN)=spotDescrip;
Exp(zoneSel).hOLexpNm(traceN)=expStr;
Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)=plateNum;
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
catch
catchissue='Ln141 EZlstBoxExt'
msg='Error'
end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
end

723
workflow/apps/matlab/ezview/EZmDayPlotUcomposite.m
View File

@@ -1,218 +1,179 @@
%***********User find and build composite of Selected Gene Composite and
%*************Plot it on OLay Plot and Trend plot DNLaxles
%***************For Chonological Studies (multi Day Studies)
%Called when Composite_ toggle button is clicked.
%Data stored for printable Trend Plot production (click [L] in DNLaxes )
%*********************
% User find and build composite of Selected Gene Composite and
% Plot it on OLay Plot and Trend plot DNLaxles
% For Chonological Studies (multi Day Studies)
% Called when Composite_ toggle button is clicked.
% Data stored for printable Trend Plot production (click [L] in DNLaxes )
global ghandles
global Exp
global exDlst
global exFolder
tracN=Exp(expN).traceN;
n= Exp(expN).DexpN; %Temp input for development
%UmDayaa= cell(3,n); UmDaybb= cell(3,n);
patrnN=strfind(selGnOrf{1},':'); %Extract Gene-Orf Name
selStrNm= char(selGnOrf)
usrGene= selStrNm(1:(patrnN(1)-1))
n=Exp(expN).DexpN; % Temp input for development
% UmDayaa=cell(3,n); UmDaybb=cell(3,n);
patrnN=strfind(selGnOrf{1},':'); % Extract Gene-Orf Name
selStrNm=char(selGnOrf)
usrGene=selStrNm(1:(patrnN(1)-1))
prompt={'Enter Specifics Term if used to futher specify selection '}
dlg_title='User Specifics Term for Refinement Composite';
num_lines=1;
def={'None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
% usrGene=cell2mat(answer(1));
usrSpec=answer(1);
usrGnSp=strcat(usrGene,usrSpec);
if strcmpi(usrSpec,'None'), usrGnSp={strcat(usrGene,'-')}; end
% if strfind(Exp(expN).UgeneSpLst,usrGnSp), break; end
Exp(expN).Dexp(n).UsrmdPLB={[]};
Exp(expN).Dexp(n).UsrMedianG=[];
Exp(expN).Dexp(n).UsrminG=[];
Exp(expN).Dexp(n).UsrmaxG=[];
Exp(expN).Dexp(n).UsrstdG=[];
Exp(expN).Dexp(n).UsrmeanG=[];
Exp(expN).Dexp(n).UsrCmpGL=[]; % For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK=[]; % For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr=[]; % For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrGLB={};
prompt={'Enter Specifics Term if used to futher specify selection '}
dlg_title='User Specifics Term for Refinement Composite';
num_lines=1;
def={'None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
%usrGene= cell2mat(answer(1));
usrSpec= answer(1);
usrGnSp= strcat(usrGene,usrSpec);
if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')}; end
for n=1:Exp(expN).DexpLength % Loop Thru Dayexps
MPnum=length(Exp(expN).Dexp(n).MP);
DMnum=length(Exp(expN).Dexp(n).DM.drug);
tPtsSize=size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3));
% lstindx=size(aa,1);
% lstindxOrf=size(bb,1);
spN=0;
rfcnt=0;
dRF1indx=0;
% usrGene=cell2mat(usrGene); %user entry of Specifics for Ref selection
usrSp=cell2mat(usrSpec); %user entry of Specifics for Ref selection
%if strfind(Exp(expN).UgeneSpLst,usrGnSp), break; end
Exp(expN).Dexp(n).UsrmdPLB= {[]};
Exp(expN).Dexp(n).UsrMedianG= [];
Exp(expN).Dexp(n).UsrminG= [];
Exp(expN).Dexp(n).UsrmaxG= [];
Exp(expN).Dexp(n).UsrstdG= [];
Exp(expN).Dexp(n).UsrmeanG= [];
Exp(expN).Dexp(n).UsrCmpGL= []; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK= []; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr= []; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrGLB= {};
for n=1:Exp(expN).DexpLength %LOOP Thru DayExps
MPnum=length(Exp(expN).Dexp(n).MP);
DMnum= length(Exp(expN).Dexp(n).DM.drug);
tPtsSize= size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3));
%*********************************
%lstindx= size(aa,1);
%lstindxOrf= size(bb,1);
spN=0;
rfcnt=0;
dRF1indx=0;
%usrGene= cell2mat(usrGene); %user entry of Specifics for Ref selection
usrSp= cell2mat(usrSpec); %user entry of Specifics for Ref selection
%*******************************************************
for mp=1:length(Exp(expN).Dexp(n).MP)
%RF1fullPlate=0;
for mp=1:length(Exp(expN).Dexp(n).MP)
% RF1fullPlate=0;
for ind384=1:384
spN=spN+1;
try %
r= ceil(ind384/24);
try
r=ceil(ind384/24);
if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
%Insert test for numeric in genename and orf if isnumeric
%Correct common EXCEL problem of converting OCT1 into a date numeric
if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991,
% Insert test for numeric in genename and orf if isnumeric
% Correct common EXCEL problem of converting OCT1 into a date numeric
if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'};
elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '};
end
%*****************************************************************
%DISPersed REFerence capture and find Medians
if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp)))...
|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
strcmpi(usrSp,'None'))) ),
% DISPersed REFerence capture and find Medians
if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ...
&& strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp))) ...
|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ...
&& strcmpi(usrSp,'None'))) )
dRF1indx=dRF1indx+1;
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)= (Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
drf(dRF1indx,2)= {strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)= mp;
drf(dRF1indx,4)={r}; drfr(dRF1indx,mp)= r;
drf(dRF1indx,5)={c}; drfc(dRF1indx,mp)= c;
drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)= ind384;
%drf(dRF1indx,7)= (Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
end %if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...
%*******************************************************************************
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)=(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
drf(dRF1indx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)=mp;
drf(dRF1indx,4)={r}; drfr(dRF1indx,mp)=r;
drf(dRF1indx,5)={c}; drfc(dRF1indx,mp)=c;
drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)=ind384;
%drf(dRF1indx,7)=(Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
end
catch
error='EZexpSel lineAfter 24 EZmultiGeneLst.m'
mp %Disable in future to prevent a bomb out OR put into a nested TryCatch
ind384 %Disable in future to prevent a bomb out OR put into a nested TryCatch
msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
end
end
mp
end
end %end associated with for ind384=1:384
mp
end %end associated with for mp=1:length(Exp(expN).Dexp(n).MP)
%*****************************************************
%************************************************************************************************
%Exp(expN).Dexp(n).UsrmdPindx=[];
%Exp(expN).Dexp(n).UsrmdPpltN=[];
if exist('drf','var')
%Det. index of change from one MP to the next
% Exp(expN).Dexp(n).UsrmdPindx=[];
% Exp(expN).Dexp(n).UsrmdPpltN=[];
if exist('drf','var')
% Det. index of change from one MP to the next
i=2;
clear chgIndx
chgIndx(1)=1;
for j=1:length(drf(:,3))
for j=1:length(drf(:,3))
if j>1
if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
if cell2mat(drf(j,3))~=cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
end
end
chgIndx(length(chgIndx)+1)= length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)= cell2mat(drf(:,3:6));
vv= zeros(length(drf),1 ); %DMnum);
%************************************
dMPs= unique(cell2mat(drf(:,3)));
%*****************************************
end
chgIndx(length(chgIndx)+1)=length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)=cell2mat(drf(:,3:6));
vv=zeros(length(drf),1 ); % DMnum);
dMPs=unique(cell2mat(drf(:,3)));
for mm=1:length(dMPs) % length(chgIndx)
usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel);
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp= NZrefIndxP;
NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp=NZrefIndxP;
vv(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
%For Global Ref Composite 17_1009 %**************************************************************************
% For Global Ref Composite 17_1009
vvK(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
vvr(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
%*****************************************************************************************************
end %for mm=1:length(dMPs)
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
uu= horzcat(uu,vv);
for d=dmSel:dmSel
end % for mm=1:length(dMPs)
% Calc. Global Mean, Std, And Median For Distributed References
uu=horzcat(uu,vv);
for d=dmSel:dmSel
medianIndxG=[];
NZusrIndxG=[];
minG=min(nonzeros(vv(:,d)));
maxG=max(nonzeros(vv(:,d)));
usrmeanG= mean(nonzeros(vv(:,d)));
usrStdG= std(nonzeros(vv(:,d)));
NZusrIndxG= find(vv(:,d));
if isempty(usrmeanG), nonZeroCntD=0, %medianIndxDisp= RFmeanG(d);
else nonZeroCntD= length(nonzeros(vv(:,d)));
usrmeanG=mean(nonzeros(vv(:,d)));
usrStdG=std(nonzeros(vv(:,d)));
NZusrIndxG=find(vv(:,d));
if isempty(usrmeanG)
nonZeroCntD=0 % medianIndxDisp=RFmeanG(d);
else
nonZeroCntD=length(nonzeros(vv(:,d)));
end
%Calc. of median value for composite doesn't require and odd number of Indx items
medianIndxG= NZusrIndxG(:);
% Calc. of median value for composite doesn't require and odd number of Indx items
medianIndxG=NZusrIndxG(:);
if ~isempty(NZusrIndxG) && length(medianIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
Exp(expN).Dexp(n).UsrGLB(d)= usrGnSp; %strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).UsrLvals= vv(medianIndxG);
Exp(expN).Dexp(n).UsrKvals= vvK(medianIndxG);
Exp(expN).Dexp(n).Usrrvals= vvr(medianIndxG);
Exp(expN).Dexp(n).UsrGLB(d)=usrGnSp; % strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).UsrLvals=vv(medianIndxG);
Exp(expN).Dexp(n).UsrKvals=vvK(medianIndxG);
Exp(expN).Dexp(n).Usrrvals=vvr(medianIndxG);
end
end
end
end
end % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
%*********************************************************************
%####################################################################
end %for n=1:Exp(expN).DexpLength %Loop thru Dayexps
Exp(expN).UgeneCnt= Exp(expN).UgeneCnt +1;
Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)= usrGnSp;
%#######################################################################
Exp(expN).UgeneCnt=Exp(expN).UgeneCnt +1;
Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)=usrGnSp;
%***********PLOT Values Selected Gene-Specifics Composite ******************************************try
smpSz= size(medianIndxG,1);
K= median(vvK(medianIndxG,dmSel)); Ks= num2str(K); Kstd= std(vvK(medianIndxG,dmSel)); KstdStr= num2str(Kstd);
r= median(vvr(medianIndxG,dmSel)); rs= num2str(r); rstd= std(vvr(medianIndxG,dmSel)); rstdStr= num2str(rstd);
l= median(vv(medianIndxG,dmSel)); Ls= num2str(l); Lstd= std(vv(medianIndxG,dmSel)); LstdStr= num2str(Lstd);
Kl= K - std(vvK(medianIndxG,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku= K + std(vvK(medianIndxG,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl= r - std(vvr(medianIndxG,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru= r + std(vvr(medianIndxG,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast= l - std(vv(medianIndxG,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow= l + std(vv(medianIndxG,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
% PLOT Values Selected Gene-Specifics Composite
smpSz=size(medianIndxG,1);
K=median(vvK(medianIndxG,dmSel)); Ks=num2str(K); Kstd=std(vvK(medianIndxG,dmSel)); KstdStr=num2str(Kstd);
r=median(vvr(medianIndxG,dmSel)); rs=num2str(r); rstd=std(vvr(medianIndxG,dmSel)); rstdStr=num2str(rstd);
l=median(vv(medianIndxG,dmSel)); Ls=num2str(l); Lstd=std(vv(medianIndxG,dmSel)); LstdStr=num2str(Lstd);
Kl=K - std(vvK(medianIndxG,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku=K + std(vvK(medianIndxG,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl=r - std(vvr(medianIndxG,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru=r + std(vvr(medianIndxG,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast=l - std(vv(medianIndxG,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow=l + std(vv(medianIndxG,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
indx=((LBr-1)*24) +LBc
MP=Exp(zoneSel).Dexp(DexpN).MP;
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
indx=((LBr-1)*24) +LBc
MP=Exp(zoneSel).Dexp(DexpN).MP;
try
t=1:200;
clear g;
try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
t=1:200;
clear g;
try
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
Exp(1).traceN=Exp(1).traceN+1;
@@ -228,150 +189,102 @@ if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
Exp(3).traceN=Exp(3).traceN+1;
traceN=Exp(3).traceN;
end
plot(plotAxes,t,g);hold (plotAxes,'on');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
%************************************************************************
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
catch
plot(plotAxes,t,g);hold (plotAxes,'on');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
% Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;
try
for i=1:length(Exp(zoneSel).hOL(:))
set(Exp(zoneSel).hOL(i),'color',[0 0 1]);
end
catch
end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
catch
catchissue='Ln100 EZlstBoxExt'
end %trycatch
end
%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
% Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'string'));end
if expN==3,DMstr=char(get(handles.DM3,'string'));end
gene=usrGnSp; orf='' % MP(1,LBmp).orf{1,1}(indx);
geneOrfstr=strcat(gene,'_',orf,'_');
grfgenestr=strcat(gene,'_',orf,'_');
gene= usrGnSp; orf= '' %MP(1,LBmp).orf{1,1}(indx);
geneOrfstr= strcat(gene,'_',orf,'_');
grfgenestr= strcat(gene,'_',orf,'_');
%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
%graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
% spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
% tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
% graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
end
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr= {xp(startPos:endPos)}
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr={xp(startPos:endPos)}
Exp(zoneSel).hOLname(traceN)= spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)= plateNum;
Exp(zoneSel).hOLname(traceN)=spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)=graphStr;
Exp(zoneSel).hOLexpNm(traceN)=expStr; %ghandles.Exp(expN).hOLexpNm(traceN)=expStr;
Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)=plateNum;
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
% traceData=vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
catch
catchissue='Ln141 EZlstBoxExt'
msg='Error'
if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
catch ME
msg='ME.message';
end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
% Deprecated functions
%{
% If a specific spot median is ever needed
%Calc. of EXACT median specific culture requires an odd number of indx items
if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)==0, medianIndxOdd= NZusrIndxG(1:(size(NZusrIndxG,1)-1)); end
if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)~=0, medianIndxOdd= NZusrIndxG(:); end
mvalsDG= median(vv(medianIndxOdd,d)); %(nonzeros(vv(:,d)));
if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)~=0, medianIndxOdd=NZusrIndxG(:); end
mvalsDG=median(vv(medianIndxOdd,d)); %(nonzeros(vv(:,d)));
nzPosIndxDG=find(mvalsDG==vv(:,d));
Exp(expN).Dexp(n).UsrMedianG(d)= mvalsDG;
Exp(expN).Dexp(n).UsrminG(d)= minG;
Exp(expN).Dexp(n).UsrmaxG(d)= maxG;
Exp(expN).Dexp(n).UsrstdG(d)= usrStdG;
Exp(expN).Dexp(n).UsrmeanG(d)= usrmeanG;
Exp(expN).Dexp(n).UsrMedianG(d)=mvalsDG;
Exp(expN).Dexp(n).UsrminG(d)=minG;
Exp(expN).Dexp(n).UsrmaxG(d)=maxG;
Exp(expN).Dexp(n).UsrstdG(d)=usrStdG;
Exp(expN).Dexp(n).UsrmeanG(d)=usrmeanG;
%}
%{
Exp(expN).Dexp(n).UsrCmpGL.dm(d).med= median(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).mean= mean(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).std= std(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).min= min(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).max= max(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).med= median(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).mean= mean(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).std= std(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).min= min(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).max= max(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).med= median(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).mean= mean(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).std= std(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).min= min(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).max= max(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).med=median(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).mean=mean(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).std=std(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).min=min(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGL.dm(d).max=max(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).med=median(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).mean=mean(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).std=std(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).min=min(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).max=max(vvK(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).med=median(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).mean=mean(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).std=std(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).min=min(vvr(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGr.dm(d).max=max(vvr(medianIndxP,d)); %For Ref Composite 17_1026
%}
%{
for mm=1:length(dMPs) % length(chgIndx)
for d= selDM:selDM %1:(DMnum)
for d=selDM:selDM %1:(DMnum)
medianIndxDisp=[];
NZrefIndxP=[];
nonZeroValsP=[];
@@ -379,56 +292,56 @@ Exp(expN).Dexp(n).UsrCmpGr.dm(d).max= max(vvr(medianIndxP,d)); %For Ref Composit
usrScNdisp=((dMPs(mm)-1)*DMnum)+(d);
try % Determine the dispersed User Gene median mean and std if such exist
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp= NZrefIndxP
NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp=NZrefIndxP
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
%For Global Ref Composite 17_1009 %**************************************************************************
vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
%*****************************************************************************************************
%{
nonZeroValsP= nonzeros(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp= std(nonZeroValsP);
mean1Disp= mean(nonZeroValsP);
minDisp= min(nonZeroValsP);
maxDisp= max(nonZeroValsP);
nonZeroValsP=nonzeros(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp=std(nonZeroValsP);
mean1Disp=mean(nonZeroValsP);
minDisp=min(nonZeroValsP);
maxDisp=max(nonZeroValsP);
drfVals=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
%nzValsAcc(mm).DM(d,:)= nonZeroValsP;
%nzValsAcc(mm).DM(d,:)=nonZeroValsP;
%MEDIAN Determination for PLATES with Dispersed RFs
%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP;
%NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp=NZrefIndxP;
else nonZeroCntDisp=length(NZrefIndxP);
end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp= NZrefIndxP(1:nonZeroCntDisp-1); end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp=NZrefIndxP; end
%}
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 0 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLstDisp= Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(medianIndxDisp,5);
medValLstDisp=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(medianIndxDisp,5);
mval1Disp=median(medValLstDisp);
nzMedPosIndx=find(mval1Disp==nonZeroValsP);
medianIndxP= NZrefIndxP(nzMedPosIndx);
%UsrmdlocP(1)= ceil(medianIndxP/24); %calc r value
%UsrmdlocP(2)= medianIndxP - ((UsrmdlocP(1)-1)*24); %calc c value
medianIndxP=NZrefIndxP(nzMedPosIndx);
%UsrmdlocP(1)=ceil(medianIndxP/24); %calc r value
%UsrmdlocP(2)=medianIndxP - ((UsrmdlocP(1)-1)*24); %calc c value
meanKval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3))));
meanrval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4))));
meanKval=mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3))));
meanrval=mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4))));
else
% Need to set L r K values to zeros or pick the first spot with zeros
%Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection'
firstZeroDindx= find(((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
medianCalcFailedD='To Few nonZero spots for valid median RF1 selection'
firstZeroDindx=find(((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
%Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroD;
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))=dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
end %~isempty(NZrefIndxP) && length(medianIndxPisp) > 3 ln584
catch %try ln565
medianCalcTryFailed1D= 'Failed! Failed! {Dispersed RF1s}'
medianCalcTryFailed1D='Failed! Failed! {Dispersed RF1s}'
try
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx= uu(firstZeroindxD,4);
firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx=uu(firstZeroindxD,4);
catch
end
end %try ~ln565
@@ -440,16 +353,16 @@ catch %try ln565
%Code Template taken from EZlstBoxCmpExt.m
try
%if RFcmpGFlg==0
smpSz= size(medianIndxP,1);
K= median(vvK(medianIndxP,dmSel)); Ks= num2str(K); Kstd= std(vvK(medianIndxP,dmSel)); KstdStr= num2str(Kstd);
r= median(vvr(medianIndxP,dmSel)); rs= num2str(r); rstd= std(vvr(medianIndxP,dmSel)); rstdStr= num2str(rstd);
l= median(vv(medianIndxP,dmSel)); Ls= num2str(l); Lstd= std(vv(medianIndxP,dmSel)); LstdStr= num2str(Lstd);
Kl= K - std(vvK(medianIndxP,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku= K + std(vvK(medianIndxP,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl= r - std(vvr(medianIndxP,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru= r + std(vvr(medianIndxP,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast= l - std(vv(medianIndxP,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow= l + std(vv(medianIndxP,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
smpSz=size(medianIndxP,1);
K=median(vvK(medianIndxP,dmSel)); Ks=num2str(K); Kstd=std(vvK(medianIndxP,dmSel)); KstdStr=num2str(Kstd);
r=median(vvr(medianIndxP,dmSel)); rs=num2str(r); rstd=std(vvr(medianIndxP,dmSel)); rstdStr=num2str(rstd);
l=median(vv(medianIndxP,dmSel)); Ls=num2str(l); Lstd=std(vv(medianIndxP,dmSel)); LstdStr=num2str(Lstd);
Kl=K - std(vvK(medianIndxP,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku=K + std(vvK(medianIndxP,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl=r - std(vvr(medianIndxP,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru=r + std(vvr(medianIndxP,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
lfast=l - std(vv(medianIndxP,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
lslow=l + std(vv(medianIndxP,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
@@ -460,12 +373,12 @@ t=1:200;
clear g;
try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
%tser=(scan(1,plateNum).plate(1).t0Series(:));
%rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
%rawData=scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
@@ -486,16 +399,16 @@ plot(plotAxes,t,g);hold (plotAxes,'on'); %plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y'); plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
Exp(expN).lstd(traceN)= std(vv(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
Exp(expN).kstd(traceN)= std(vvK(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Exp(expN).rstd(traceN)= std(vvr(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
Exp(expN).lstd(traceN)=std(vv(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
Exp(expN).kstd(traceN)=std(vvK(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Exp(expN).rstd(traceN)=std(vvr(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
Exp(expN).lKl(traceN)= Kl; Exp(expN).Ku(traceN)= Ku;
Exp(expN).lrl(traceN)= rl; Exp(expN).Ku(traceN)= ru;
Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;
Exp(expN).lKl(traceN)=Kl; Exp(expN).Ku(traceN)=Ku;
Exp(expN).lrl(traceN)=rl; Exp(expN).Ku(traceN)=ru;
%************************************************************************
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
@@ -509,12 +422,12 @@ end %trycatch
%if expN==1,DMstr=char(get(handles.DM1,'string'));end
%if expN==2,DMstr=char(get(handles.DM2,'string'));end
%if expN==3,DMstr=char(get(handles.DM3,'string'));end
DMstr= num2str(dmSel);
DMstr=num2str(dmSel);
%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
%graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
%graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
spotDescrip=strcat(graphStr,'DMS->',DMstr);
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
@@ -526,14 +439,14 @@ end
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr= {xp(startPos:endPos)}
expStr={xp(startPos:endPos)}
Exp(zoneSel).hOLname(traceN)= usrGnSp; %spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
%Exp(zoneSel).hOLplateNum(traceN)= plateNum;
Exp(zoneSel).hOLname(traceN)=usrGnSp; %spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)=graphStr;
Exp(zoneSel).hOLexpNm(traceN)=expStr; %ghandles.Exp(expN).hOLexpNm(traceN)=expStr;
Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
%Exp(zoneSel).hOLplateNum(traceN)=plateNum;
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
%traceData=vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
%if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
%if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
@@ -570,106 +483,106 @@ end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot
%{
%elseif RFcmpGFlg==1
K= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks= num2str(K);
r= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs= num2str(r);
l= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls= num2str(l);
Kl= K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Ku= K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
rl= r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
ru= r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
lfast= l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
lslow= l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
K=Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks=num2str(K);
r=Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs=num2str(r);
l=Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls=num2str(l);
Kl=K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Ku=K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
rl=r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
ru=r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
lfast=l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
lslow=l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
end
%}
%Exp(expN).Dexp(n).UsrmdPindx= [];
%Exp(expN).Dexp(n).UsrmdPpltN= [];
%Exp(expN).Dexp(n).UsrmdPscanN= [];
%Exp(expN).Dexp(n).UsrMedianP= [];
%Exp(expN).Dexp(n).stdP= [];
%Exp(expN).Dexp(n).meanP= [];
%Exp(expN).Dexp(n).minP= [];
%Exp(expN).Dexp(n).maxP= [];
%Exp(expN).Dexp(n).UsrmdPindx=[];
%Exp(expN).Dexp(n).UsrmdPpltN=[];
%Exp(expN).Dexp(n).UsrmdPscanN=[];
%Exp(expN).Dexp(n).UsrMedianP=[];
%Exp(expN).Dexp(n).stdP=[];
%Exp(expN).Dexp(n).meanP=[];
%Exp(expN).Dexp(n).minP=[];
%Exp(expN).Dexp(n).maxP=[];
%Exp(expN).Dexp(n).RFmdGLB= {[]};
%Exp(expN).Dexp(n).RFmdGindx= [];
%Exp(expN).Dexp(n).RFmdGpltN= [];
%Exp(expN).Dexp(n).RFmdGscanN= [];
%Exp(expN).Dexp(n).RFmdGLB={[]};
%Exp(expN).Dexp(n).RFmdGindx=[];
%Exp(expN).Dexp(n).RFmdGpltN=[];
%Exp(expN).Dexp(n).RFmdGscanN=[];
%UsrmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
%UsrmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
%UsrmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
%UsrmdDGloc(d,1)=uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
%UsrmdDGloc(d,2)=uu(nzPosIndxDG,2); %calc r value
%UsrmdDGloc(d,3)=uu(nzPosIndxDG,3); %calc c value
%lstindx=lstindx+1;
%lstindxOrf= lstindxOrf+1;
%lstindxOrf=lstindxOrf+1;
%{
usrGLbl= strcat(usrGnSp,'UmdG('); %accomodate User Ref Selection
aa(lstindx,1)= strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
aa(lstindx,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)= strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
bb(lstindxOrf,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
usrGLbl=strcat(usrGnSp,'UmdG('); %accomodate User Ref Selection
aa(lstindx,1)=strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
aa(lstindx,2)={strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)=strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
bb(lstindxOrf,2)={strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
%Composite Reference Amalgum Plot ******************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')');
lstindxOrf=lstindxOrf+1;
aa(lstindx,1)=strcat(usrGnSp,'UcmpG(',num2str(d),')');
aa(lstindx,2)={''};
bb(lstindxOrf,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')');
bb(lstindxOrf,1)=strcat(usrGnSp,'UcmpG(',num2str(d),')');
bb(lstindxOrf,2)={''};
%*****************************************************
%}
%{
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
usrPLbl= strcat(usrGnSp,'UmdP('); %accomodate User Ref Selection
aa(lstindx,1)= strcat(usrPLbl,num2str(d),')');
aa(lstindx,2)= {strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};
bb(lstindxOrf,1)= strcat(usrPLbl,num2str(d),')'); %remove string2cell brackets {...}
lstindxOrf=lstindxOrf+1;
usrPLbl=strcat(usrGnSp,'UmdP('); %accomodate User Ref Selection
aa(lstindx,1)=strcat(usrPLbl,num2str(d),')');
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};
bb(lstindxOrf,1)=strcat(usrPLbl,num2str(d),')'); %remove string2cell brackets {...}
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};
Exp(expN).Dexp(n).UsrmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))= medianIndxP;
Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(n).UsrmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=medianIndxP;
Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))=dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(n).UsrmdPscanN(d,dMPs(mm))=usrScNdisp;
Exp(expN).Dexp(n).UsrMedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(n).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(n).meanP(d,dMPs(mm))= mean1Disp;
Exp(expN).Dexp(n).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(n).maxP(d,dMPs(mm))= maxDisp;
Exp(expN).Dexp(n).UsrMedianP(d,dMPs(mm))=mval1Disp;
Exp(expN).Dexp(n).stdP(d,dMPs(mm))=std1Disp;
Exp(expN).Dexp(n).meanP(d,dMPs(mm))=mean1Disp;
Exp(expN).Dexp(n).minP(d,dMPs(mm))=minDisp;
Exp(expN).Dexp(n).maxP(d,dMPs(mm))=maxDisp;
Exp(expN).Dexp(n).UsrCmpPL.dm(d).med= mval1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).mean= mean1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).std= std1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).min= minDisp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).max= maxDisp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).med=mval1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).mean=mean1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).std=std1Disp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).min=minDisp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPL.dm(d).max=maxDisp; %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).med=median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).mean=mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).std=std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).min=min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).max=max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).med=median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).mean=mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).std=std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).min=min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPr.dm(d).max=max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
%}
%Exp(expN).Dexp(n).UsrmdGindx(d)= nzPosIndxDG;
%Exp(expN).Dexp(n).UsrmdGpltN(d)= UsrmdDGloc(d,1);
%Exp(expN).Dexp(n).UsrmdGscanN(d)= uu(nzPosIndxDG,4);
%Exp(expN).Dexp(n).UsrmdGindx(d)=nzPosIndxDG;
%Exp(expN).Dexp(n).UsrmdGpltN(d)=UsrmdDGloc(d,1);
%Exp(expN).Dexp(n).UsrmdGscanN(d)=uu(nzPosIndxDG,4);
%{
try
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx= uu(firstZeroindxD,4);
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx=uu(firstZeroindxD,4);
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))=dMPs(mm);
%Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroPindx;
catch
catchissue='try at Ln565'
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))=dMPs(mm);
%Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
end
try
% Exp(expN).Dexp(n).UsrmdPpltN= dMPs(mm);
% Exp(expN).Dexp(n).UsrmdPpltN=dMPs(mm);
catch
catchissue='Ln619'
%Exp(expN).Dexp(n).UsrmdPpltN= 1; %This might keep from breaking BUT ???
%Exp(expN).Dexp(n).UsrmdPpltN=1; %This might keep from breaking BUT ???
end
error='EZexpSel lineAfter 565'
end %try ~ln565

444
workflow/apps/matlab/ezview/EZmDayTrend.m
View File

@@ -1,47 +1,41 @@
%GraphicDestinationPertibationComparison**15_821
%Called by EZlstBoxExt or EZvDatatip.m, Then calls EZRFs4DayComp
CompositeTrendFlg=0;
if expN==1 && get(ghandles.CompositeTog1,'value')==1 ||...
expN==2 && get(ghandles.CompositeTog2,'value')==1 ||...
expN==3 && get(ghandles.CompositeTog3,'value')==1.
% GraphicDestinationPertibationComparison**15_821
% Called by EZlstBoxExt or EZvDatatip.m, Then calls EZRFs4DayComp
CompositeTrendFlg=0;
if expN==1 && get(ghandles.CompositeTog1,'value')==1 ...
|| expN==2 && get(ghandles.CompositeTog2,'value')==1 ...
|| expN==3 && get(ghandles.CompositeTog3,'value')==1
CompositeTrendFlg=1;
end
%if (isequal(destcompMsg,'GoodDataTip')&&~isequal(destcompMsg, 'BadDataTip'))|| isequal(destcompMsg,'Olay')
%hold off
if expN==1,DexpN= (get(ghandles.DN1,'value')); end
if expN==2,DexpN= (get(ghandles.DN2,'value')); end
if expN==3,DexpN= (get(ghandles.DN3,'value')); end
if expN==1,MPsel=floor(get(ghandles.MPsldr1,'value')); end
if expN==2,MPsel=floor(get(ghandles.MPsldr2,'value')); end
if expN==3,MPsel=floor(get(ghandles.MPsldr3,'value')); end
if expN==1,pertSel=floor(get(ghandles.DMsldr1,'value')); end
if expN==2,pertSel=floor(get(ghandles.DMsldr2,'value')); end
if expN==3,pertSel=floor(get(ghandles.DMsldr3,'value')); end
dmSel= pertSel;
end
% if (isequal(destcompMsg,'GoodDataTip')&&~isequal(destcompMsg, 'BadDataTip'))|| isequal(destcompMsg,'Olay')
% hold off
if expN==1,DexpN=(get(ghandles.DN1,'value')); end
if expN==2,DexpN=(get(ghandles.DN2,'value')); end
if expN==3,DexpN=(get(ghandles.DN3,'value')); end
if expN==1,MPsel=floor(get(ghandles.MPsldr1,'value')); end
if expN==2,MPsel=floor(get(ghandles.MPsldr2,'value')); end
if expN==3,MPsel=floor(get(ghandles.MPsldr3,'value')); end
if expN==1,pertSel=floor(get(ghandles.DMsldr1,'value')); end
if expN==2,pertSel=floor(get(ghandles.DMsldr2,'value')); end
if expN==3,pertSel=floor(get(ghandles.DMsldr3,'value')); end
dmSel=pertSel;
if EZdatatip==1 %adaptation for image spot selection
%plNums= plateNum;
destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
plNums= (MPsel-1)*destPerMP + (1:destPerMP);
%plNums=plateNum;
destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
plNums=(MPsel-1)*destPerMP + (1:destPerMP);
zoneSel=expN;
tracN=Exp(zoneSel).traceN;
if zoneSel==1,Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1; end
if zoneSel==2,Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2; end
if zoneSel==3,Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3; end
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end
elseif EZdatatip==2 %adaption for Overlay plot selection
destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
MPlateN= ceil(OLplateNum/destPerMP);
plNums= (MPlateN-1)*destPerMP + (1:destPerMP);
elseif EZdatatip==2 % adaption for Overlay plot selection
destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
MPlateN=ceil(OLplateNum/destPerMP);
plNums=(MPlateN-1)*destPerMP + (1:destPerMP);
zoneSel=expN;
tracN=Exp(zoneSel).traceN;
if zoneSel==1,Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1; end
@@ -50,18 +44,17 @@ elseif EZdatatip==2 %adaption for Overlay plot selection
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end %2016_0222
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end %2016_0222
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end %2016_0222
elseif EZdatatip==0
if lstBoxCmpFlg~=1
%destPerMP= Exp(expN).Dexp(DexpN).destPerMP;
plNums= (LBmp-1)*destPerMP + (1:destPerMP);
% destPerMP=Exp(expN).Dexp(DexpN).destPerMP;
plNums=(LBmp-1)*destPerMP + (1:destPerMP);
tracN=Exp(zoneSel).traceN;
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end %2016_0222
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end %2016_0222
if zoneSel==3,DNLaxes=ghandles.DNLaxes3;end %2016_0222
elseif lstBoxCmpFlg==1
%DexpN= Exp(expN).DexpN;
dmSel= pertSel;
% DexpN=Exp(expN).DexpN;
dmSel=pertSel;
tracN=Exp(zoneSel).traceN;
if zoneSel==1,DNLaxes=ghandles.DNLaxes1;end %2016_0222
if zoneSel==2,DNLaxes=ghandles.DNLaxes2;end %2016_0222
@@ -69,21 +62,18 @@ elseif EZdatatip==0
end
end
if EZdatatip==2 %Response to Overlay click
%++++++++++++++++++++LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL+++++++++++++++++++++++
%seltraceN comes from EZvDatatip;
%Exp(OLay).seltraceN iscaptured from EZvDatatip
if EZdatatip==2 % Response to Overlay click
% seltraceN comes from EZvDatatip;
% Exp(OLay).seltraceN iscaptured from EZvDatatip
% if an OLay trace is selected
% else it is captured below if EZdatatip is not equal to 2
try
set(Exp(zoneSel).hLRF1(seltraceN),'visible','on'); set(Exp(zoneSel).hLRF2(seltraceN),'visible','on');
catch, end
try
set(Exp(zoneSel).hL(seltraceN),'visible','on'); set(Exp(zoneSel).hLb(seltraceN),'visible','on');
catch, end
%Plot new intL
% Plot new intL
try
set(Exp(zoneSel).hintL(seltraceN),'visible','on'); set(Exp(zoneSel).hintLb(seltraceN),'visible','on');
catch, end
@@ -92,7 +82,7 @@ if EZdatatip==2 %Response to Overlay click
catch, end
if zoneSel==1,set(ghandles.DNLaxes1,'xlim',[-75,75]); end
%++++++++++++++++++++++KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK++++++++++++++++++++++
% K values
for J=1:(tracN),
try
set(Exp(zoneSel).hKRF1(J),'visible','off'); set(Exp(zoneSel).hKRF2(J),'visible','off');
@@ -107,8 +97,7 @@ if EZdatatip==2 %Response to Overlay click
try
set(Exp(zoneSel).hK(seltraceN),'visible','on'); set(Exp(zoneSel).hKb(seltraceN),'visible','on');
catch, end
%+++++++++++++++++++++rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr+++++++++++++++++++++++++++++
for J=1:(tracN),
for J=1:(tracN)
try
set(Exp(zoneSel).hrRF1(J),'visible','off'); set(Exp(zoneSel).hrRF2(J),'visible','off');
catch, end
@@ -122,9 +111,8 @@ if EZdatatip==2 %Response to Overlay click
try
set(Exp(zoneSel).hr(seltraceN),'visible','on'); set(Exp(zoneSel).hrb(seltraceN),'visible','on');
catch, end
else %if EZdatatip==1 or if EZdatatip==0 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%Attempt fix for overlaying L and intL from image datatip==1 18_0103
else % if EZdatatip==1 or if EZdatatip==0
% Attempt fix for overlaying L and intL from image datatip==1 18_0103
try
set(Exp(zoneSel).hLRF1(seltraceN),'visible','off'); set(Exp(zoneSel).hLRF2(seltraceN),'visible','off');
catch, end
@@ -132,7 +120,7 @@ else %if EZdatatip==1 or if EZdatatip==0 ++++++++++++++++++++++++++++++++++++++
set(Exp(zoneSel).hL(seltraceN),'visible','off'); set(Exp(zoneSel).hLb(seltraceN),'visible','off');
catch, end
%Plot new intL
% Plot new intL
try
set(Exp(zoneSel).hintL(seltraceN),'visible','off'); set(Exp(zoneSel).hintLb(seltraceN),'visible','off');
catch, end
@@ -140,58 +128,46 @@ else %if EZdatatip==1 or if EZdatatip==0 ++++++++++++++++++++++++++++++++++++++
set(Exp(zoneSel).hintLadj(seltraceN),'visible','off'); set(Exp(zoneSel).hintLadjb(seltraceN),'visible','off');
catch, end
%*************Plot RFmd1 and RFmd2 indexes*********************
if lstBoxCmpFlg~= 1 % If selection is a "normal" item with a location in the label
days= Exp(expN).DexpLength;
for nn=1:Exp(expN).DexpLength %length(Exp(zoneSel).Dexp)
RFconfig= Exp(zoneSel).Dexp(DexpN).RFconfig;
%*****************************
EZRFs4DayComp %***************
%*****************************
if lstBoxCmpFlg~= 1
% Plot RFmd1 and RFmd2 indexes
if lstBoxCmpFlg~=1 % If selection is a "normal" item with a location in the label
days=Exp(expN).DexpLength;
for nn=1:Exp(expN).DexpLength % length(Exp(zoneSel).Dexp)
RFconfig=Exp(zoneSel).Dexp(DexpN).RFconfig;
EZRFs4DayComp
if lstBoxCmpFlg~=1
Exp(zoneSel).seltraceN=tracN;
seltraceN=tracN;
end
%**************Plot L K r for all Day pertibation(XdestinationX) Plates***************
try RF1mdNums= (RF1mdPltN-1)*destPerMP + (pertSel); catch, end %RF1mdPltN %
try RF2mdNums= (RF2mdPltN-1)*destPerMP + (pertSel); catch, end %RF2mdPltN %
% Plot L K r for all Day pertibation(XdestinationX) Plates
try RF1mdNums=(RF1mdPltN-1)*destPerMP + (pertSel); catch, end % RF1mdPltN
try RF2mdNums=(RF2mdPltN-1)*destPerMP + (pertSel); catch, end % RF2mdPltN
if CompositeTrendFlg==0 || EZdatatip==1
lvals(nn)=Exp(zoneSel).Dexp(nn).scan(1,plNums(pertSel)).plate(1).CFout(indx,5);
if lvals(nn)==0, lvals(nn)=140; end
kvals(nn)=Exp(zoneSel).Dexp(nn).scan(1,plNums(pertSel)).plate(1).CFout(indx,3);
rvals(nn)=Exp(zoneSel).Dexp(nn).scan(1,plNums(pertSel)).plate(1).CFout(indx,4);
Exp(expN).Trace(traceN).dmSel= pertSel;
Exp(expN).Trace(traceN).UsrGLB= selGnOrf; %usrGnSp;
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).UsrLvals= lvals(nn);
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).UsrKvals= kvals(nn);
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).Usrrvals= rvals(nn);
elseif CompositeTrendFlg==1 && EZdatatip==0 %Gene-Specifics Composite from listBox
days= Exp(expN).DexpLength;
Exp(expN).Trace(traceN).dmSel=pertSel;
Exp(expN).Trace(traceN).UsrGLB=selGnOrf; %usrGnSp;
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).UsrLvals=lvals(nn);
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).UsrKvals=kvals(nn);
Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).Usrrvals=rvals(nn);
elseif CompositeTrendFlg==1 && EZdatatip==0 % Gene-Specifics Composite from listBox
days=Exp(expN).DexpLength;
if iscell(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals)
lvals(nn)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
if lvals(nn)==0, lvals(nn)=140; end
kvals(nn)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrKvals));
rvals(nn)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).Usrrvals));
kvals(nn)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrKvals));
rvals(nn)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).Usrrvals));
else
lvals(nn)=median(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals);
if lvals(nn)==0, lvals(nn)=140; end
kvals(nn)= median(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrKvals);
rvals(nn)= median(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).Usrrvals);
kvals(nn)=median(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrKvals);
rvals(nn)=median(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).Usrrvals);
end
end
end %if CompositeTrendFlg==0 || EZdatatip==1
try
%lvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx(nn),5);
lvalsRF1md(nn)= RFmdVal(nn); %RFmdVal(nn) gets the above if 'F', or the global median if 'G' or the local median if 'L' selected
% lvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx(nn),5);
lvalsRF1md(nn)=RFmdVal(nn); %RFmdVal(nn) gets the above if 'F', or the global median if 'G' or the local median if 'L' selected
if lvalsRF1md(nn)==0, lvalsRF1md(nn)=140; end
kvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx,3);
rvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx,4);
@@ -206,120 +182,97 @@ Exp(expN).Trace(tracN).Dexp(nn).DM(pertSel).Usrrvals= rvals(nn);
end
try
if (~exist('lvalsRF1md','var')||~exist('lvalsRF2md','var'))&& exist('RFcmpGFlg','var') && RFcmpGFlg==1
lvalsRF1md(nn)= Exp(expN).DexpN(nn).RFcmpGL.DM(dmSel);
lvalsRF1md(nn)=Exp(expN).DexpN(nn).RFcmpGL.DM(dmSel);
if lvalsRF2md(nn)==0, lvalsRF2md(nn)=140; end
end
lvalsRF1md(nn)= RFmdVal(nn); %RFmdVal(nn) gets the above if 'F', or the global median if 'G' or the local median if 'L' selected
lvalsRF1md(nn)=RFmdVal(nn); %RFmdVal(nn) gets the above if 'F', or the global median if 'G' or the local median if 'L' selected
if lvalsRF1md(nn)==0, lvalsRF1md(nn)=140; end
kvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx,3);
rvalsRF1md(nn)=Exp(zoneSel).Dexp(nn).scan(1,RF1mdNums).plate(1).CFout(RF1mdIndx,4);
catch
end
%Added for INTERACTION Calculating Utility 2016_0219
% Added for INTERACTION Calculating Utility 2016_0219
try
if CompositeTrendFlg==0 || EZdatatip==1 %18_0103 Add || EZdatatip==1
Xn(nn)= Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,5);
Xln(nn)= Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,11);
Xhn(nn)= Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,12);
elseif CompositeTrendFlg==1 && EZdatatip==0 %18_0103 add && EZdatatip==0 Gene-Specifics Composite from listBox
Xn(nn)= median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
Xln(nn)= Xn(nn) - std(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
Xhn(nn)= Xn(nn) + std(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
if CompositeTrendFlg==0 || EZdatatip==1 % 18_0103 Add || EZdatatip==1
Xn(nn)=Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,5);
Xln(nn)=Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,11);
Xhn(nn)=Exp(expN).Dexp(nn).scan(plNums(pertSel)).plate(1).CFout(indx,12);
elseif CompositeTrendFlg==1 && EZdatatip==0 % 18_0103 add && EZdatatip==0 Gene-Specifics Composite from listBox
Xn(nn)=median(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
Xln(nn)=Xn(nn) - std(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
Xhn(nn)=Xn(nn) + std(cell2mat(Exp(expN).Trace(tracN).Dexp(nn).DM(dmSel).UsrLvals));
end
if Xn(nn)==0, deltaXR(nn)= 140; end
if Xn(nn)==0, deltaXR(nn)=140; end
if isnan(Xhn(nn))||isnan(Xln(nn))|| Xhn(nn)==0||Xln(nn)==0||isnan(Rs(nn))
deltaXR(nn)= 140;
elseif Xn(nn) >= Rn(nn)
deltaXR(nn)= Xln(nn)-(Rn(nn)+Rs(nn));
deltaXR(nn)=140;
elseif Xn(nn) >=Rn(nn)
deltaXR(nn)=Xln(nn)-(Rn(nn)+Rs(nn));
else
deltaXR(nn)= Xhn(nn)-(Rn(nn)-Rs(nn));
deltaXR(nn)=Xhn(nn)-(Rn(nn)-Rs(nn));
end
catch
msg= 'No Refs! ->No Interaction Calculations!'
msg='No Refs! ->No Interaction Calculations!'
end
end %for nn=1:Exp(expN).DexpLength
%**************************ELSEIF
elseif lstBoxCmpFlg==1 %Determine values of RF1cmp or RFcmpG
days= Exp(expN).DexpLength;
if strcmp(Exp(expN).DexpType,'chrono'), DM= inDM; else DM= pertSel; end %else DM= dmSel;
Exp(zoneSel).seltraceN=tracN; %added fix 2020_1103
seltraceN=tracN; %added fix 2020_1103
for nn=1:Exp(expN).DexpLength %length(Exp(zoneSel).Dexp)
RFconfig= Exp(zoneSel).Dexp(DexpN).RFconfig;
%*****************************
EZRFs4DayComp %***************
%*****************************
if RFcmpGFlg==0 %RF1cmp or RF2cmp clicked
lvals(nn)= Exp(expN).Dexp(nn).RFcmpL(RFnum).dm(DM).med;
end
elseif lstBoxCmpFlg==1 % determine values of RF1cmp or RFcmpG
days=Exp(expN).DexpLength;
if strcmp(Exp(expN).DexpType,'chrono'), DM=inDM; else DM=pertSel; end % else DM=dmSel;
Exp(zoneSel).seltraceN=tracN; % added fix 2020_1103
seltraceN=tracN; % added fix 2020_1103
for nn=1:Exp(expN).DexpLength % length(Exp(zoneSel).Dexp)
RFconfig=Exp(zoneSel).Dexp(DexpN).RFconfig;
EZRFs4DayComp
if RFcmpGFlg==0 % RF1cmp or RF2cmp clicked
lvals(nn)=Exp(expN).Dexp(nn).RFcmpL(RFnum).dm(DM).med;
if lvals(nn)==0, lvals(dm)=140; end
kvals(nn)= Exp(expN).Dexp(nn).RFcmpK(RFnum).dm(DM).med;
rvals(nn)= Exp(expN).Dexp(nn).RFcmpr(RFnum).dm(DM).med;
kvals(nn)=Exp(expN).Dexp(nn).RFcmpK(RFnum).dm(DM).med;
rvals(nn)=Exp(expN).Dexp(nn).RFcmpr(RFnum).dm(DM).med;
elseif RFcmpGFlg==1
lvals(nn)= Exp(expN).Dexp(nn).RFcmpGL.dm(DM).med;% Ls= num2str(l);
lvals(nn)=Exp(expN).Dexp(nn).RFcmpGL.dm(DM).med; % Ls=num2str(l);
if lvals(nn)==0, lvals(nn)=140; end
kvals(nn)= Exp(expN).Dexp(nn).RFcmpGK.dm(DM).med; %Ks= num2str(K);
rvals(nn)= Exp(expN).Dexp(nn).RFcmpGr.dm(DM).med; %rs= num2str(r);
kvals(nn)=Exp(expN).Dexp(nn).RFcmpGK.dm(DM).med; % Ks=num2str(K);
rvals(nn)=Exp(expN).Dexp(nn).RFcmpGr.dm(DM).med; % rs=num2str(r);
end
%Added for INTERACTION Calculating Utility 2016_0219
% Added for INTERACTION Calculating Utility 2016_0219
try
Xn(nn)=lvals(nn);
try
Xln(nn)= lvals(nn)- Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(DM).std ;
Xhn(nn)= lvals(nn)+ Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(DM).std;
Xln(nn)=lvals(nn)- Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(DM).std ;
Xhn(nn)=lvals(nn)+ Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(DM).std;
catch
Xln(nn)= lvals(nn)- Exp(expN).Dexp(DexpN).RFcmpGL.dm(DM).std ;
Xhn(nn)= lvals(nn)+ Exp(expN).Dexp(DexpN).RFcmpGL.dm(DM).std;
Xln(nn)=lvals(nn)- Exp(expN).Dexp(DexpN).RFcmpGL.dm(DM).std ;
Xhn(nn)=lvals(nn)+ Exp(expN).Dexp(DexpN).RFcmpGL.dm(DM).std;
end
if Xn(nn)==0, deltaXR(nn)= 140; end
if Xn(nn)==0, deltaXR(nn)=140; end
if isnan(Xhn(nn))||isnan(Xln(nn))|| Xhn(nn)==0||Xln(nn)==0||isnan(Rs(nn))
deltaXR(nn)= 140;
elseif Xn(nn) >= Rn(nn)
deltaXR(nn)= Xln(nn)-(Rn(nn)+Rs(nn));
deltaXR(nn)=140;
elseif Xn(nn) >=Rn(nn)
deltaXR(nn)=Xln(nn)-(Rn(nn)+Rs(nn));
else
deltaXR(nn)= Xhn(nn)-(Rn(nn)-Rs(nn));
deltaXR(nn)=Xhn(nn)-(Rn(nn)-Rs(nn));
end
catch
msg= 'No Refs! ->No Interaction Calculations!'
msg='No Refs! ->No Interaction Calculations!'
end
end
end
end % Second for nn loop lstBoxCmpFlg==1 %for nn=1:Exp(expN).DexpLength
end %if lstBoxCmpFlg~= 1
%end
%///////////////////////////////////////////////////////////////////
%XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
%***********INTERACTION Plotting Utility 2016_0219*********************************************
try
if Rn(1)==0, % If Ref mean is zero
intL= 0; proGrIntL=0; intLadj=0; proGrIntLadj=0;
% Interaction Plotting Utility 2016_0219
try
if Rn(1)==0 % If Ref mean is zero
intL=0; proGrIntL=0; intLadj=0; proGrIntLadj=0;
intNormL=6.66;intNormLadj=6.66; proGrIntNormL=6.66;proGrIntNormLadj=6.66;
else
%if Xn(pertSel)==0 || Xn(pertSel)==140,intL =140; else intL=(Xn-Rn); end
intL= (Xn-Rn);
intL(Xn==0)= 140;
intLadj=(deltaXR);
Exp(expN).Trace(tracN).Dexp(DexpN).UsrIntL= intL;
end
catch
FailMessage= 'Problem with Reference Rn value; Unable to produce Interaction values! Ln119 EZdestComp'
end
else
% if Xn(pertSel)==0 || Xn(pertSel)==140,intL=140; else intL=(Xn-Rn); end
intL=(Xn-Rn);
intL(Xn==0)=140;
intLadj=(deltaXR);
Exp(expN).Trace(tracN).Dexp(DexpN).UsrIntL=intL;
end
catch
FailMessage='Problem with Reference Rn value; Unable to produce Interaction values! Ln119 EZdestComp'
end
hidem(ghandles.Daxes1)
if zoneSel==1,showm(ghandles.Dlaxes1);showm(ghandles.Dkaxes1);showm(ghandles.Draxes1);end
@@ -333,17 +286,16 @@ end
if zoneSel==3,showm(ghandles.DNLaxes3); end
set(DNLaxes,'NextPlot','add');
%+++++++++++++++++LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL+++++++++++++++++++++++++++++++++
%Make visible the current L plot and store it for retrieval by OLay code
%Plot RF1 and/or RF2 OR if No RF1-RF2 Plot RFcmpGL
% Make visible the current L plot and store it for retrieval by OLay code
% Plot RF1 and/or RF2 OR if No RF1-RF2 Plot RFcmpGL
try %Some experiments do not have ref. plates
Exp(zoneSel).hLRF1(tracN)= plot(Dlaxes,lvalsRF1md,1:days,'y'); hold on
Exp(zoneSel).hLRF1(tracN)=plot(Dlaxes,lvalsRF1md,1:days,'y'); hold on
catch1=0;
catch
catch1=1;
end
try
Exp(zoneSel).hLRF2(tracN)= plot(Dlaxes,lvalsRF2md,1:days,'y'); hold on
Exp(zoneSel).hLRF2(tracN)=plot(Dlaxes,lvalsRF2md,1:days,'y'); hold on
catch2=0;
catch
catch2=1;
@@ -351,42 +303,38 @@ end
try
if catch1 && catch2&& RFcmpGFlg==1
for nn=1:Exp(expN).DexpLength
lvalsRF1md(nn)= Exp(1,expN).Dexp(1,nn).RFcmpGL.dm(1,dmSel).med;
lvalsRF1md(nn)=Exp(1,expN).Dexp(1,nn).RFcmpGL.dm(1,dmSel).med;
if lvalsRF1md(nn)==0, lvalsRF1md(nn)=140; end
end
end
Exp(zoneSel).hLRF1(tracN)= plot(Dlaxes,lvalsRF1md,1:days,'y');
Exp(zoneSel).hLRF1(tracN)=plot(Dlaxes,lvalsRF1md,1:days,'y');
catch
end
%************************************************************
%Plot USER SELECTION DATA**************************************
% Plot User Selection Data
try
Exp(zoneSel).hL(tracN)= plot(Dlaxes,lvals,1:days); Exp(zoneSel).hLb(tracN)= plot(Dlaxes,lvals,1:days,'rs');
Exp(zoneSel).hL(tracN)=plot(Dlaxes,lvals,1:days); Exp(zoneSel).hLb(tracN)=plot(Dlaxes,lvals,1:days,'rs');
catch
end
%*************************************************************
if zoneSel==1,set(ghandles.Dlaxes1,'xlim',[0,140]); end
if zoneSel==2,set(ghandles.Dlaxes2,'xlim',[0,140]); end
if zoneSel==3,set(ghandles.Dlaxes3,'xlim',[0,140]); end
%*************************************************
%Make visible Plot for Interaction Data, Store and Hide unless a N (InteractionPBsel) set that plot on Top of the RawData Plots.
%Plot new intL
% Make visible Plot for Interaction Data, Store and Hide unless a N (InteractionPBsel) set that plot on Top of the RawData Plots.
% Plot new intL
try
% zeroCLn= zeros(1,days)
% zeroCLn=zeros(1,days)
% Exp(zoneSel).hzeroCLn=plot(DNLaxes,zeroCLn,1:days,'y');
Exp(zoneSel).hintL(tracN)= plot(DNLaxes,intL,1:days); Exp(zoneSel).hintLb(tracN)= plot(DNLaxes,intL,1:days,'rs');
Exp(zoneSel).hintLadj(tracN)= plot(DNLaxes,intLadj,1:days,'g'); Exp(zoneSel).hintLadjb(tracN)= plot(DNLaxes,intLadj,1:days,'gs');
catch,
Exp(zoneSel).hintL(tracN)= plot(DNLaxes,intL,1:days); Exp(zoneSel).hintLb(tracN)=plot(DNLaxes,intL,1:days,'rs');
Exp(zoneSel).hintLadj(tracN)= plot(DNLaxes,intLadj,1:days,'g'); Exp(zoneSel).hintLadjb(tracN)=plot(DNLaxes,intLadj,1:days,'gs');
catch
end
if zoneSel==1,set(ghandles.DNLaxes1,'xlim',[-75,75]); end
if zoneSel==2,set(ghandles.DNLaxes2,'xlim',[-75,75]); end
if zoneSel==3,set(ghandles.DNLaxes3,'xlim',[-75,75]); end
%+++++++++++++++++KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK+++++++++++++++++++++++++++++++++++++++++++++++++++++++
%Hide all K plots
for J=1:(tracN-1),
% Hide all K plots
for J=1:(tracN-1)
try
set(Exp(zoneSel).hKRF1(J),'visible','off'); set(Exp(zoneSel).hKRF2(J),'visible','off');
catch, end
@@ -394,20 +342,20 @@ end
set(Exp(zoneSel).hK(J),'visible','off'); set(Exp(zoneSel).hKb(J),'visible','off');
catch, end
end
%Make visible the current L plot and store it for retrieval by OLay code
try %Some experiments do not have ref. plates
Exp(zoneSel).hKRF1(tracN)= plot(Dkaxes,kvalsRF1md,1:days,'y');
Exp(zoneSel).hKRF2(tracN)= plot(Dkaxes,kvalsRF2md,1:days,'y');
% Make visible the current L plot and store it for retrieval by OLay code
try % Some experiments do not have ref. plates
Exp(zoneSel).hKRF1(tracN)=plot(Dkaxes,kvalsRF1md,1:days,'y');
Exp(zoneSel).hKRF2(tracN)=plot(Dkaxes,kvalsRF2md,1:days,'y');
catch, end
try
Exp(zoneSel).hK(tracN)= plot(Dkaxes,kvals,1:days); Exp(zoneSel).hKb(tracN)= plot(Dkaxes,kvals,1:days,'rs');
Exp(zoneSel).hK(tracN)= plot(Dkaxes,kvals,1:days); Exp(zoneSel).hKb(tracN)=plot(Dkaxes,kvals,1:days,'rs');
catch, end
set(Dkaxes,'xlim',[0,200]) %max(kvals+20)
set(Dkaxes,'xlim',[0,200]) % max(kvals+20)
set(Dkaxes,'ycolor',[.9,.9,1])
%++++++++++++++++++rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr+++++++++++++++++++++++++++++++++++++++++++++++
%Hide all r plots
for J=1:(tracN-1),
% Hide all r plots
for J=1:(tracN-1)
try
set(Exp(zoneSel).hrRF1(J),'visible','off'); set(Exp(zoneSel).hrRF2(J),'visible','off');
catch, end
@@ -415,49 +363,44 @@ end
set(Exp(zoneSel).hr(J),'visible','off'); set(Exp(zoneSel).hrb(J),'visible','off');
catch, end
end
%Make visible the current r plot and store it for retrieval by OLay code
try %Some experiments do not have ref. plates
Exp(zoneSel).hrRF1(tracN)= plot(Draxes,rvalsRF1md,1:days,'y');
Exp(zoneSel).hrRF2(tracN)= plot(Draxes,rvalsRF2md,1:days,'y');
% Make visible the current r plot and store it for retrieval by OLay code
try % Some experiments do not have ref. plates
Exp(zoneSel).hrRF1(tracN)=plot(Draxes,rvalsRF1md,1:days,'y');
Exp(zoneSel).hrRF2(tracN)=plot(Draxes,rvalsRF2md,1:days,'y');
catch, end
try
Exp(zoneSel).hr(tracN)= plot(Draxes,rvals,1:days); Exp(zoneSel).hrb(tracN)= plot(Draxes,rvals,1:days,'rs');
Exp(zoneSel).hr(tracN)= plot(Draxes,rvals,1:days); Exp(zoneSel).hrb(tracN)=plot(Draxes,rvals,1:days,'rs');
catch, end
set(Draxes,'xlim',[0,1])
set(Draxes,'ycolor',[.9,.9,1])
end %if EZdatatip==2 Response to Overlay click
if CompositeTrendFlg==1 && EZdatatip~=0
% lbLKr= strcat(gene,'_',spec,'_');
drug= Exp(expN).Dexp(DexpN).DM.drug{dmSel};
conc= Exp(expN).Dexp(DexpN).DM.conc{dmSel};
media= Exp(expN).Dexp(DexpN).DM.media{dmSel};
mod1= Exp(expN).Dexp(DexpN).DM.mod1{dmSel};
conc1= Exp(expN).Dexp(DexpN).DM.conc1{dmSel};
mod2= Exp(expN).Dexp(DexpN).DM.mod2{dmSel};
conc2=Exp(expN).Dexp(DexpN).DM.conc2{dmSel};
dmStr= strcat(drug,conc,'_',media,'_',mod1,conc1,mod2,conc2);
grfgenestr= strcat(grfgenestr,dmStr);
end
if zoneSel==1, set(ghandles.geneOrfLKr1,'string', grfgenestr);end
if zoneSel==2, set(ghandles.geneOrfLKr2,'string', grfgenestr);end
if zoneSel==3, set(ghandles.geneOrfLKr3,'string', grfgenestr);end
if CompositeTrendFlg==1 && EZdatatip~=0
% lbLKr=strcat(gene,'_',spec,'_');
drug=Exp(expN).Dexp(DexpN).DM.drug{dmSel};
conc=Exp(expN).Dexp(DexpN).DM.conc{dmSel};
media=Exp(expN).Dexp(DexpN).DM.media{dmSel};
mod1=Exp(expN).Dexp(DexpN).DM.mod1{dmSel};
conc1=Exp(expN).Dexp(DexpN).DM.conc1{dmSel};
mod2=Exp(expN).Dexp(DexpN).DM.mod2{dmSel};
conc2=Exp(expN).Dexp(DexpN).DM.conc2{dmSel};
dmStr=strcat(drug,conc,'_',media,'_',mod1,conc1,mod2,conc2);
grfgenestr=strcat(grfgenestr,dmStr);
end
if zoneSel==1, set(ghandles.geneOrfLKr1,'string', grfgenestr);end
if zoneSel==2, set(ghandles.geneOrfLKr2,'string', grfgenestr);end
if zoneSel==3, set(ghandles.geneOrfLKr3,'string', grfgenestr);end
%*********************************************************************************************************************
%*********************************************************************************************************************
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%___________________________________Display Selection PlotFilter ____________________
% Display Selection PlotFilter
if lstBoxCmpFlg~= 1,
seltraceN= Exp(zoneSel).seltraceN
end
if EZdatatip==0, seltraceN= tracN; end
if Exp(4).interacPBsel==0 %00000000000000000000000000000
if lstBoxCmpFlg~=1,
seltraceN=Exp(zoneSel).seltraceN
end
if EZdatatip==0, seltraceN=tracN; end
if Exp(4).interacPBsel==0
% replace ghandles.DNLaxes1 (Dlaxes2)etc. with a single
% Exp(zoneSel).DNLaxes,....
set(ghandles.Dlaxes1,'Visible','on')
@@ -474,7 +417,6 @@ end
try
set(Exp(zoneSel).hL(n),'visible','off'); set(Exp(zoneSel).hLb(n),'visible','off');
catch, end
try
set(Exp(zoneSel).hintL(n),'visible','off'); set(Exp(zoneSel).hintLb(n),'visible','off');
catch, end
@@ -492,10 +434,7 @@ end
for i=1:Exp(zoneSel).expLoadCnt,
try set(Exp(zoneSel).hzeroCLn(i),'visible','off'); catch ME, end
end
elseif Exp(4).interacPBsel==1 %111111111111111111111111111
elseif Exp(4).interacPBsel==1
set(ghandles.DNLaxes1,'Visible','on')
set(ghandles.DNLaxes2,'Visible','on')
set(ghandles.DNLaxes3,'Visible','on')
@@ -503,7 +442,6 @@ end
set(ghandles.Dlaxes2,'Visible','off')
set(ghandles.Dlaxes3,'Visible','off')
for n=1:Exp(zoneSel).traceN
try set(Exp(zoneSel).hLRF1(n),'visible','off'); catch, end
try set(Exp(zoneSel).hLRF2(n),'visible','off'); catch, end
@@ -513,27 +451,14 @@ end
end
try set(Exp(zoneSel).hintL(seltraceN),'visible','on'); set(Exp(zoneSel).hintLb(seltraceN),'visible','on'); catch, end
try set(Exp(zoneSel).hintLadj(seltraceN),'visible','on'); set(Exp(zoneSel).hintLadjb(seltraceN),'visible','on'); catch, end
for i=1:Exp(zoneSel).expLoadCnt,
for i=1:Exp(zoneSel).expLoadCnt
try set(Exp(zoneSel).hzeroCLn(i),'visible','on'); catch ME, end
end
elseif Exp(4).interacPBsel==2 %2222222222222222222222222222 TEMPorily Same as interacPBsel==1
% set(ghandles.DNLaxes1,'Visible','on')
%set(ghandles.Dlaxes1,'Visible','off')
end %if Exp(4).interacPBsel==0
%pause(2)
%------------------------------------------------------------------------------------------------------------
%=====================================================================================================================
%end %if isempty(msg)
elseif Exp(4).interacPBsel==2
end
%{
%Attempt fix for overlaying L and intL from image datatip==1 18_0103
% Attempt fix for overlaying L and intL from image datatip==1 18_0103
if Exp(4).interacPBsel==0 %0000
try
set(Exp(zoneSel).hLRF1(seltraceN),'visible','off'); set(Exp(zoneSel).hLRF2(seltraceN),'visible','off');
@@ -543,7 +468,7 @@ end
catch, end
end
%Hide intL
% Hide intL
if Exp(4).interacPBsel==1 %1111
try
set(Exp(zoneSel).hintL(seltraceN),'visible','off'); set(Exp(zoneSel).hintLb(seltraceN),'visible','off');
@@ -552,7 +477,6 @@ end
set(Exp(zoneSel).hintLadj(seltraceN),'visible','off'); set(Exp(zoneSel).hintLadjb(seltraceN),'visible','off');
catch, end
end
%}

12
workflow/apps/matlab/ezview/EZmultiDay.m
View File

@@ -8,8 +8,8 @@ d=strfind(exDlst,'_');
clear expDlstS
ii=0;
for n=1:(size(c,1))
if ((sum(ismember(cell2mat(c(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(c(n)),[3,4]))) ||...
(sum(ismember(cell2mat(d(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(d(n)),[3,4]))))
if ((sum(ismember(cell2mat(c(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(c(n)),[3,4]))) ...
|| (sum(ismember(cell2mat(d(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(d(n)),[3,4]))))
ii=ii+1;
expDlst(ii)=exDlst(n);
end
@@ -17,7 +17,7 @@ end
clear matFile
ii=0;
for m= 1:size(expDlst,2)
for m=1:size(expDlst,2)
exD=fullfile(exFolder,cell2mat(expDlst(m)))
dirLst=dir(exD);
clear matFlst
@@ -31,7 +31,7 @@ for m= 1:size(expDlst,2)
matFlst=dir(resMatF)
for o=1:size(matFlst,1)
if sum(ismember('.mat', matFlst(o).name))==4
ii= ii+1;
ii=ii+1;
resDir{ii}=fullfile(exFolder,cell2mat(expDlst(m)),resF)
matFile(m)=cellstr(fullfile(resMatF,matFlst(o).name))
end
@@ -40,6 +40,6 @@ for m= 1:size(expDlst,2)
end
end
Exp(expN).DexpLength= size(matFile,2);
Exp(expN).DexpN= size(matFile,2);
Exp(expN).DexpLength=size(matFile,2);
Exp(expN).DexpN=size(matFile,2);

54
workflow/apps/matlab/ezview/EZmultiDayExp.m
View File

@@ -1,28 +1,25 @@
% Is the callback supposed to be nested?
function EZmultiDayGui
%global Exp
global exDlst
%global Exp
global exDlst
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
spacing=0.02;% Spacing between the button and the next command's label
%====================================
% The ADD Groups button
btnNumber=1;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
%fhImParm=gcf;
exFolder=uigetdir
exDirs=dir(exFolder)
exFs={exDirs.name}
%====================================
exFolder=uigetdir
exDirs=dir(exFolder)
exFs= {exDirs.name}
f=figure('Menubar','none','Position',[1000 100 640 750],'Name','Select Exp Folders' );
hListbox=uicontrol(...
f=figure('Menubar','none','Position',[1000 100 640 750],'Name','Select Exp Folders' );
hListbox=uicontrol(...
'Style', 'listbox',...
'String',sort(exFs),...
'value',[],...
@@ -30,38 +27,35 @@ hListbox=uicontrol(...
'min',1,...
'Units','normalized',...
'Position', [.70 .40 .6 .60],...
'callback',{@load_listbox}); %'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,eventdata)
%global CSrchRng
%global CSrearchRange
userIndx=(get(source,'value'))
userStr=(get(source,'string'))
%scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx)
exDlst= user_entry
'callback',{@load_listbox}); % 'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,eventdata)
% global CSrchRng
% global CSrearchRange
userIndx=(get(source,'value'))
userStr=(get(source,'string'))
% scLstIndx=str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx)
exDlst=user_entry
end
exFs
btnNumber=10;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit8=uicontrol(...
hedit8=uicontrol(...
'Style', 'pushbutton',...
'String',{'Continue'},...
'Units','normalized',...
'Position', btnPos,...
'callback','uiresume(gcbf)');
uiwait(gcf);
uiwait(gcf);
close(f)
close(f)
end
%*******************
%EZmultiDay
%*****************************************************************
% EZmultiDay

4
workflow/apps/matlab/ezview/EZmultiDayGui.m
View File

@@ -1,4 +1,4 @@
% EZmultiDayGui.m called by EZexpSel.m ln957 && ln963
% EZmultiDayGui.m called by EZexpSel.m
% EZmultiday is called after this EZmultiDayGui.m also by EZexpSel.m
function EZmultiDayGui
@@ -42,7 +42,7 @@ function EZmultiDayGui
j=1;
for i=1:size(CC,1)
j=CC(i,2);
ExpOrderByExp(i)= expDayFs(j); %exFs(j)
ExpOrderByExp(i)=expDayFs(j); %exFs(j)
end
else
ExpOrderByExp=sort(exFs);

381
workflow/apps/matlab/ezview/EZmultiExLoad.m
View File

@@ -1,5 +1,6 @@
%EZmultiExLoad
%Calls to EZVimDisplay (ln 185) EZmultiGeneRFsLst (ln213) EZdiagRFsSheet(ln218)
% EZmultiExLoad
% Calls to EZVimDisplay (ln 185) EZmultiGeneRFsLst (ln213) EZdiagRFsSheet(ln218)
% TODO this file could use some elseif's
global Exp
global zonePB
@@ -11,283 +12,264 @@ global exFolder
% Load .mat file
expN=zonePB; % added to accomodate AppDesigner limitations 230821
Exp(expN).UgeneCnt=0;
Exp(expN).DexpLength= size(matFile,2); DexpLength= size(matFile,2);
for n=1:Exp(expN).DexpLength %size(matFile,2)
if expN==1
Exp(expN).DexpLength=size(matFile,2); DexpLength=size(matFile,2);
for n=1:Exp(expN).DexpLength % size(matFile,2)
if expN==1
orfLstSel=get(handles.GeneOrfTog,'value');
end
if expN==2
end
if expN==2
orfLstSel=get(handles.GeneOrfTog,'value');
end
if expN==3
end
if expN==3
orfLstSel=get(handles.GeneOrfTog,'value');
end
Exp(expN).Dexp(n).srtGnLst={('CheckMP/MPDMfile')};
Exp(expN).Dexp(n).srtOrfLst={('CheckMP/MPDMfile')};
set(handles.listboxGnOrf,'value',1) %Fix accomodation for bug in App Designer .. .wlapp converter 230918
set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
%try
ExpOutmat= matFile(n) %fullfile(scansDir,openExpfile);
end
Exp(expN).Dexp(n).srtGnLst={('CheckMP/MPDMfile')};
Exp(expN).Dexp(n).srtOrfLst={('CheckMP/MPDMfile')};
set(handles.listboxGnOrf,'value',1) %Fix accomodation for bug in App Designer .. .wlapp converter 230918
set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
% try
ExpOutmat=matFile(n) %fullfile(scansDir,openExpfile);
load(char(ExpOutmat));
%cd(scansDir)
%cd ..;
%resDir=pwd;
Exp(expN).Dexp(n).resDir= cell2mat(resDir(n));
Exp(expN).Dexp(n).resDir=cell2mat(resDir(n));
cd(Exp(expN).Dexp(n).resDir)
cd ..;
ExpPath=pwd;
Exp(expN).Dexp(n).ExpFoldr= ExpPath;
Exp(expN).Dexp(n).ExpFoldr=ExpPath;
cd(w)
%Experiment LOADs
load(fullfile(Exp(expN).Dexp(n).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','Coordinates'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','anlZones'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','BGatTpts'))
load(fullfile(Exp(expN).Dexp(n).resDir,'PTmats','NImParameters'))
%Backup for cond. sothat failure to load is recovered back prev. ExpJob data
%test in temp
Exp(expN).Dexp(n).temp.DM=DM;
Exp(expN).Dexp(n).temp.MP=MP;
Exp(expN).Dexp(n).temp.scan=scan;
Exp(expN).Dexp(n).temp.FexpScanSpots=FexpScanSpots;
Exp(expN).Dexp(n).temp.FexpScanBMtp=FexpScanBMtp;
Exp(expN).Dexp(n).temp.anlZoneRefs=anlZoneRefs;
Exp(expN).Dexp(n).temp.ImParMat=ImParMat;
Exp(expN).Dexp(n).DM=Exp(expN).Dexp(n).temp.DM;
Exp(expN).Dexp(n).MP= Exp(expN).Dexp(n).temp.MP;
Exp(expN).Dexp(n).scan= Exp(expN).Dexp(n).temp.scan;
Exp(expN).Dexp(n).FexpScanSpots= Exp(expN).Dexp(n).temp.FexpScanSpots;
Exp(expN).Dexp(n).FexpScanBMtp= Exp(expN).Dexp(n).temp.FexpScanBMtp;
Exp(expN).Dexp(n).anlZoneRefs=Exp(expN).Dexp(n).temp.anlZoneRefs;
Exp(expN).Dexp(n).ImParMat=Exp(expN).Dexp(n).temp.ImParMat;
% Experiment LOADs
load(fullfile(Exp(expN).Dexp(n).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','Coordinates'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','anlZones'))
load(fullfile(Exp(expN).Dexp(n).resDir,'Fotos','BGatTpts'))
load(fullfile(Exp(expN).Dexp(n).resDir,'PTmats','NImParameters'))
% Backup for cond. sothat failure to load is recovered back prev. ExpJob data
% test in temp
Exp(expN).Dexp(n).temp.DM=DM;
Exp(expN).Dexp(n).temp.MP=MP;
Exp(expN).Dexp(n).temp.scan=scan;
Exp(expN).Dexp(n).temp.FexpScanSpots=FexpScanSpots;
Exp(expN).Dexp(n).temp.FexpScanBMtp=FexpScanBMtp;
Exp(expN).Dexp(n).temp.anlZoneRefs=anlZoneRefs;
Exp(expN).Dexp(n).temp.ImParMat=ImParMat;
Exp(expN).Dexp(n).DM=Exp(expN).Dexp(n).temp.DM;
Exp(expN).Dexp(n).MP=Exp(expN).Dexp(n).temp.MP;
Exp(expN).Dexp(n).scan=Exp(expN).Dexp(n).temp.scan;
Exp(expN).Dexp(n).FexpScanSpots=Exp(expN).Dexp(n).temp.FexpScanSpots;
Exp(expN).Dexp(n).FexpScanBMtp=Exp(expN).Dexp(n).temp.FexpScanBMtp;
Exp(expN).Dexp(n).anlZoneRefs=Exp(expN).Dexp(n).temp.anlZoneRefs;
Exp(expN).Dexp(n).ImParMat=Exp(expN).Dexp(n).temp.ImParMat;
Exp(expN).Dexp((Exp(expN).DexpLength+1):end)=[];
Exp(expN).Dexp(n).temp=[];
end
Exp(expN).Dexp((Exp(expN).DexpLength+1):end)= [];
Exp(expN).Dexp(n).temp= [];
% Load First new ExpJOb
if expN==1
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
set(handles.MPsldr1,'max',MPnum); %length(MP)
set(handles.DMsldr1,'max',length(DM.drug));
set(handles.Tptsldr1,'max',tPtsSize);
end %for n=1:size(matFile,2)
%Load First new ExpJOb*****************
if expN==1,
tPtsSize= size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
set(handles.MPsldr1,'max',MPnum); %length(MP)
set(handles.DMsldr1,'max',length(DM.drug));
set(handles.Tptsldr1,'max',tPtsSize);
% MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr1,'min',1,'max',MPnum)
DMnum=length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr1,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr1,'min',1,'max',tPtsSize)
%MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr1,'min',1,'max',MPnum)
DMnum= length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr1,'min',1,'max',DMnum)
tPtsSize= size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr1,'min',1,'max',tPtsSize)
set(handles.MPsldr1,'value',1)
set(handles.DMsldr1,'value',1)
set(handles.Tptsldr1,'value',1)
set(handles.MPed1,'string','1')
set(handles.DMed1,'string','1')
set(handles.Tpted1,'string','1')
set(handles.MPsldr1,'SliderStep',[1/MPnum 1/MPnum]); % [1/length(MP) 1/length(MP)])
set(handles.DMsldr1,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr1,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.MPsldr1,'value',1)
set(handles.DMsldr1,'value',1)
set(handles.Tptsldr1,'value',1)
set(handles.MPed1,'string','1')
set(handles.DMed1,'string','1')
set(handles.Tpted1,'string','1')
set(handles.MPsldr1,'SliderStep',[1/MPnum 1/MPnum]); %[1/length(MP) 1/length(MP)])
set(handles.DMsldr1,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr1,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.DN1,'value',1)
set(handles.DN1,'string',1)
set(handles.DN1,'value',1)
set(handles.DN1,'string',1)
end
if expN==2,
tPtsSize= size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
set(handles.MPsldr2,'max',MPnum);
set(handles.DMsldr2,'max',length(DM.drug));
set(handles.Tptsldr2,'max',tPtsSize);
%MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr2,'min',1,'max',MPnum) %length(MP))
DMnum= length(Exp(expN).Dexp(n).DM.drug);
set(handles.DMsldr2,'min',1,'max',DMnum)
tPtsSize= size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr2,'min',1,'max',tPtsSize)
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); % size(FexpScanBMtp{1,1},3);
set(handles.MPsldr2,'max',MPnum);
set(handles.DMsldr2,'max',length(DM.drug));
set(handles.Tptsldr2,'max',tPtsSize);
% MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr2,'min',1,'max',MPnum) % length(MP))
DMnum=length(Exp(expN).Dexp(n).DM.drug);
set(handles.DMsldr2,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr2,'min',1,'max',tPtsSize)
set(handles.MPsldr2,'value',1)
set(handles.DMsldr2,'value',1)
set(handles.Tptsldr2,'value',1)
set(handles.MPed2,'string','1')
set(handles.DMed2,'string','1')
set(handles.Tpted2,'string','1')
set(handles.MPsldr2,'SliderStep',[1/MPnum 1/MPnum]); %1/length(MP) 1/length(MP)])
set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.MPsldr2,'value',1)
set(handles.DMsldr2,'value',1)
set(handles.Tptsldr2,'value',1)
set(handles.MPed2,'string','1')
set(handles.DMed2,'string','1')
set(handles.Tpted2,'string','1')
set(handles.MPsldr2,'SliderStep',[1/MPnum 1/MPnum]); %1/length(MP) 1/length(MP)])
set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.DN2,'value',1)
set(handles.DN2,'string',1)
set(handles.DN2,'value',1)
set(handles.DN2,'string',1)
end
if expN==3,
%Exp(3).traceN=0;
tPtsSize= size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
set(handles.MPsldr3,'max',MPnum);
set(handles.DMsldr3,'max',length(DM.drug));
set(handles.Tptsldr3,'max',tPtsSize);
%MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr3,'min',1,'max',MPnum)
DMnum= length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr3,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr3,'min',1,'max',tPtsSize)
set(handles.MPsldr3,'value',1)
set(handles.DMsldr3,'value',1)
set(handles.Tptsldr3,'value',1)
set(handles.MPed3,'string','1')
set(handles.DMed3,'string','1')
set(handles.Tpted3,'string','1')
set(handles.MPsldr3,'SliderStep',[1/MPnum 1/MPnum]); %1/length(MP) 1/length(MP)])
set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.DN3,'value',1)
set(handles.DN3,'string',1)
if expN==3
% Exp(3).traceN=0;
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3)); % size(FexpScanBMtp{1,1},3);
set(handles.MPsldr3,'max',MPnum);
set(handles.DMsldr3,'max',length(DM.drug));
set(handles.Tptsldr3,'max',tPtsSize);
% MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr3,'min',1,'max',MPnum)
DMnum=length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr3,'min',1,'max',DMnum)
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr3,'min',1,'max',tPtsSize)
set(handles.MPsldr3,'value',1)
set(handles.DMsldr3,'value',1)
set(handles.Tptsldr3,'value',1)
set(handles.MPed3,'string','1')
set(handles.DMed3,'string','1')
set(handles.Tpted3,'string','1')
set(handles.MPsldr3,'SliderStep',[1/MPnum 1/MPnum]); % 1/length(MP) 1/length(MP)])
set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);
set(handles.DN3,'value',1)
set(handles.DN3,'string',1)
end
if expN==1,set(handles.GeneOrfLoc1,'string',{''});
if expN==1
set(handles.GeneOrfLoc1,'string',{''});
set(handles.graphStrLoc1,'string',{''});
cla(handles.Paxes1)
end
if expN==2,set(handles.GeneOrfLoc2,'string',{''});
if expN==2
set(handles.GeneOrfLoc2,'string',{''});
set(handles.graphStrLoc2,'string',{''});
cla(handles.Paxes2)
end
if expN==3,set(handles.GeneOrfLoc3,'string',{''});
if expN==3
set(handles.GeneOrfLoc3,'string',{''});
set(handles.graphStrLoc3,'string',{''})
cla(handles.Paxes3)
end
Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
set(handles.listboxGnOrf,'value',1) %Fix accomodation for bug in App Designer .. .wlapp converter 230918
set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtGnLst)
set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtOrfLst)
%--------------------------------------------------------------------------
EZVimDisplay
%*********************
EZVimDisplay %*
%*********************
usrRefFg=0;
prompt={'Enter GeneName to use as Reference:',...
usrRefFg=0;
prompt={'Enter GeneName to use as Reference:',...
'Enter Specifics Term if used to futher specify Reference '}
dlg_title='User Reference Input';
num_lines=1;
def={'RF1','None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
if iscell(answer(1))
rfGene= cell2mat(answer(1));
else
rfGene= answer(1);
end
dlg_title='User Reference Input';
num_lines=1;
def={'RF1','None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
if iscell(answer(1))
rfGene=cell2mat(answer(1));
else
rfGene=answer(1);
end
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
rfSpec= answer(2); %if strcmpi(answer(2),'None'), rfSpec= ''; end
rfGnSp= strcat(rfGene,rfSpec);
if strcmpi(rfSpec,'None'), rfGnSp= {strcat(rfGene,'-')}; end
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
rfSpec=answer(2); % if strcmpi(answer(2),'None'), rfSpec=''; end
rfGnSp=strcat(rfGene,rfSpec);
if strcmpi(rfSpec,'None'), rfGnSp={strcat(rfGene,'-')}; end
%Added 17-1023 For User Addition of Gene Composites to ListBox
Expaa{expN,1}= []; Expbb{expN,1}= [];
% Added 17-1023 For User Addition of Gene Composites to ListBox
Expaa{expN,1}=[]
Expbb{expN,1}=[];
for n=1:size(matFile,2)
%*********************************************************************
try
EZmultiGeneRFsLst %**
catch
try
EZmultiGeneRFsLst
catch
msg='EZmultiGeneRFLst failed possibly Too Few non-zero Median spots'
end
%*********************************************************
EZdiagRFsSheet %**
%********************
Exp(expN).Dexp(n).RFrnames=rnames;
Exp(expN).Dexp(n).RFdata= data;
%*********************************************************
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(n).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG'))&&...
isempty(Exp(expN).Dexp(n).RFmeanG)
end
EZdiagRFsSheet
Exp(expN).Dexp(n).RFrnames=rnames;
Exp(expN).Dexp(n).RFdata=data;
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG')) ...
&& isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))==0 ||...
isempty(Exp(expN).Dexp(n).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG'))&&...
~isempty(Exp(expN).Dexp(n).RFmeanG)
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))==0 ...
|| isempty(Exp(expN).Dexp(n).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(n).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG'))&&...
~isempty(Exp(expN).Dexp(n).RFmeanG)
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=3;
end
Exp(expN).RFconfig= RFconfig;
Exp(expN).Dexp(n).RFconfig= RFconfig;
%**********************************************
try msgBadGeneName, catch, end
try
end
Exp(expN).RFconfig=RFconfig;
Exp(expN).Dexp(n).RFconfig=RFconfig;
try msgBadGeneName
catch, end
try
Exp(expN).Dexp(n).resetHtmpTg =5; %Exp(expN).resetHtmpTg =5;
if RFconfig==0,
RFconfigMsg= 'No RF1 references in this Experiment Job'
if RFconfig==0
RFconfigMsg='No RF1 references in this Experiment Job'
Exp(expN).Dexp(n).resetHtmpTg =3; %Exp(expN).resetHtmpTg =3;
end
catch
catch
end
end
%***************************
%*********************************************************************
end
%###############################################################################
%********Auto select Zone and load listboxGnOrf data**********
% Auto Select Zone And Load Listboxgnorf Data
DexpN=1;
zeroCLn= zeros(1,DMnum);
Exp(expN).expLoadCnt= Exp(expN).expLoadCnt+1; expLdCnt= Exp(expN).expLoadCnt;
if expN==1 %Adapted to accomodate AppDesigner 230821
zeroCLn=zeros(1,DMnum);
Exp(expN).expLoadCnt=Exp(expN).expLoadCnt+1; expLdCnt=Exp(expN).expLoadCnt;
if expN==1 % Adapted to accomodate AppDesigner 230821
set(handles.zonePB1,'value',1)
set(handles.zonePB2,'value',0)
set(handles.zonePB3,'value',0)
set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6])
set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0])
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
orfLstSel=get(handles.GeneOrfTog,'value')
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtOrfLst)
else
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
end
DNLaxes1= handles.DNLaxes1;
DNLaxes1=handles.DNLaxes1;
Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
end
if expN==2 %Adapted to accomodate AppDesigner 230821
if expN==2 % Adapted to accomodate AppDesigner 230821
set(handles.zonePB1,'value',0)
set(handles.zonePB3,'value',0)
set(handles.zonePB2,'value',1)
set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6])
set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0])
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
orfLstSel= get(handles.GeneOrfTog,'value');
orfLstSel=get(handles.GeneOrfTog,'value');
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtOrfLst)
else
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
end
DNLaxes2= handles.DNLaxes2;
DNLaxes2=handles.DNLaxes2;
Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
end
if expN==3 %Adapted to accomodate AppDesigner 230821
if expN==3 % Adapted to accomodate AppDesigner 230821
set(handles.zonePB1,'value',0)
set(handles.zonePB2,'value',0)
set(handles.zonePB3,'value',1)
@@ -300,7 +282,7 @@ if expN==3 %Adapted to accomodate AppDesigner 230821
else
set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
end
DNLaxes3= handles.DNLaxes3;
DNLaxes3=handles.DNLaxes3;
Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
end
@@ -314,9 +296,8 @@ if Exp(4).interacPBsel==0 %if interaction "raw" don't show a center line
end
end
%***************************
% HtMapTog 'string', 'Current user L/N' selection'
Exp(expN).Dexp(DexpN).spotIndx= [];
Exp(expN).Dexp(DexpN).spotIndx=[];
if expN==1,
Exp(1).htmapPBsel=0;
set(handles.HtMapTog1,'string','L')
@@ -334,5 +315,3 @@ if expN==3,
end
htMapTogPBfg=0;
%*******************************************************************

966
workflow/apps/matlab/ezview/EZmultiGeneRFsLst.m
View File

File diff suppressed because it is too large Load Diff

92
workflow/apps/matlab/ezview/EZsingleExUserRF.m
View File

@@ -1,42 +1,36 @@
%EZsingleExUserRF
% EZsingleExUserRF
global exp
usrRefFg=0;
prompt={'Enter GeneName to use as Reference:',...
usrRefFg=0;
prompt={'Enter GeneName to use as Reference:',...
'Enter Specifics Term if used to futher specify Reference '}
dlg_title='User Reference Input';
num_lines=1;
def={'RF1','None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
rfGene= cell2mat(answer(1));
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
rfSpec= answer(2); %if strcmpi(answer(2),'None'), rfSpec= ''; end
rfGnSp= strcat(rfGene,rfSpec);
if strcmpi(rfSpec,'None'), rfGnSp= strcat(rfGene,'-'); end
dlg_title='User Reference Input';
num_lines=1;
def={'RF1','None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
rfGene=cell2mat(answer(1));
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
rfSpec=answer(2); %if strcmpi(answer(2),'None'), rfSpec=''; end
rfGnSp=strcat(rfGene,rfSpec);
if strcmpi(rfSpec,'None'), rfGnSp=strcat(rfGene,'-'); end
%for n=1:size(matFile,2)
% for n=1:size(matFile,2)
n=1;
%*********************************************************************
EZmultiGeneRFsLst %**
%*********************************************************
EZdiagRFsSheet %**
%********************
EZmultiGeneRFsLst
EZdiagRFsSheet
Exp(expN).Dexp(n).RFrnames=rnames;
Exp(expN).Dexp(n).RFdata= data;
%*********************************************************
Exp(expN).Dexp(n).RFdata=data;
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(n).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG'))&&...
isempty(Exp(expN).Dexp(n).RFmeanG)
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG')) ...
&& isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))==0 ||...
isempty(Exp(expN).Dexp(n).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG'))&&...
~isempty(Exp(expN).Dexp(n).RFmeanG)
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))==0 ...
|| isempty(Exp(expN).Dexp(n).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmeanG')) ...
&& ~isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))&&...
@@ -45,31 +39,22 @@ if sum(ismember(fieldnames(Exp(expN).Dexp(n)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(n).RFmeanG)
RFconfig=3;
end
Exp(expN).RFconfig= RFconfig;
Exp(expN).Dexp(n).RFconfig= RFconfig;
%**********************************************
Exp(expN).RFconfig=RFconfig;
Exp(expN).Dexp(n).RFconfig=RFconfig;
try msgBadGeneName, catch, end
try
Exp(expN).Dexp(n).resetHtmpTg =5; %Exp(expN).resetHtmpTg =5;
if RFconfig==0,
RFconfigMsg= 'No RF1 references in this Experiment Job'
RFconfigMsg='No RF1 references in this Experiment Job'
Exp(expN).Dexp(n).resetHtmpTg =3; %Exp(expN).resetHtmpTg =3;
end
catch
end
%***************************
%*********************************************************************
%end
%###############################################################################
%}
%********Auto select Zone and load listboxGnOrf data**********
% Auto select Zone and load listboxGnOrf data
DexpN=1;
zeroCLn= zeros(1,DMnum);
Exp(expN).expLoadCnt= Exp(expN).expLoadCnt+1; expLdCnt= Exp(expN).expLoadCnt;
zeroCLn=zeros(1,DMnum);
Exp(expN).expLoadCnt=Exp(expN).expLoadCnt+1; expLdCnt=Exp(expN).expLoadCnt;
if expN==1
set(handles.zoneRad1,'value',1)
set(handles.zoneRad2,'value',0)
@@ -80,7 +65,7 @@ if expN==1
else
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
end
DNLaxes1= handles.DNLaxes1;
DNLaxes1=handles.DNLaxes1;
Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
end
@@ -88,15 +73,14 @@ if expN==2
set(handles.zoneRad1,'value',0)
set(handles.zoneRad3,'value',0)
set(handles.zoneRad2,'value',1)
orfLstSel= get(handles.GeneOrfTog,'value');
orfLstSel=get(handles.GeneOrfTog,'value');
if orfLstSel==1
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtOrfLst)
else
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
end
DNLaxes2= handles.DNLaxes2;
DNLaxes2=handles.DNLaxes2;
Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
end
if expN==3
@@ -109,24 +93,22 @@ if expN==3
else
set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
end
DNLaxes3= handles.DNLaxes3;
DNLaxes3=handles.DNLaxes3;
Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
end
if Exp(4).interacPBsel==0 %if interaction "raw" don't show a center line
if Exp(4).interacPBsel==0 % if interaction "raw" don't show a center line
for i=1:Exp(expN).expLoadCnt,
try
set(Exp(expN).hzeroCLn(i),'visible','off');
catch
catchissue='Ln521'
i
end
end
end
%***************************
% HtMapTog 'string', 'Current user L/N' selection'
Exp(expN).Dexp(DexpN).spotIndx= [];
Exp(expN).Dexp(DexpN).spotIndx=[];
if expN==1,
Exp(1).htmapPBsel=0;
set(handles.HtMapTog1,'string','L')
@@ -143,5 +125,3 @@ if expN==3,
EZhtMap
end
htMapTogPBfg=0;
%*******************************************************************

303
workflow/apps/matlab/ezview/EZspotview.m
View File

@@ -1,14 +1,12 @@
function EZspotview(expN,DexpN, imLoc,OLresDir,OLplateNum,NoOLay)
datacursormode(gcf)
global Exp
global ghandles
w=pwd;
aCnt=0;
prevExp=0;
if NoOLay==0
global Exp
global ghandles
datacursormode(gcf)
w=pwd;
aCnt=0;
prevExp=0;
if NoOLay==0
cd(fullfile(char(OLresDir)))
cd ..
expDir=pwd;
@@ -21,40 +19,34 @@ if NoOLay==0
if prevExp==0
expDir=Exp(expN).Dexp(DexpN).ExpFoldr;
else
cd(fullfile(char(OLresDir)))
cd ..
expDir=pwd;
cd(w)
%expDir=fullfile(char(OLresDir),'..');
end
else
else
expDir=Exp(expN).Dexp(DexpN).ExpFoldr
end
end
%ExpHmDir= char(Exp(expN).Dexp(DexpN).resDir);
try close(ghandles.hfstrip), catch, end %hfIm
%*************CIRCLE related*************************
doCircle=1;
radius=14;
diaExt=2*(radius+1);
%>>>>>>>>>>>>>>>>>>>>>>
EZvNIcircle
%<<<<<<<<<<<<<<<<<<<<<<<
%ExpHmDir=char(Exp(expN).Dexp(DexpN).resDir);
rIm= imLoc(1); %use the "picture/Image' r and c not the plate annotation r c)
cIm= imLoc(2);
plateNum= Exp(expN).Dexp(DexpN).plateNum;
%*****************************************
if prevExp==0
FexpScanSpots=Exp(expN).Dexp(DexpN).FexpScanSpots;
FexpScanBMtp=Exp(expN).Dexp(DexpN).FexpScanBMtp;
anlZoneRefs=Exp(expN).Dexp(DexpN).anlZoneRefs;
ImParMat=Exp(expN).Dexp(DexpN).ImParMat;
else
%check if the request expJob is already loaded in one of the other zones
try close(ghandles.hfstrip), catch, end % hfIm
% CIRCLE related
doCircle=1;
radius=14;
diaExt=2*(radius+1);
EZvNIcircle
rIm=imLoc(1); % use the "picture/Image' r and c not the plate annotation r c)
cIm=imLoc(2);
plateNum=Exp(expN).Dexp(DexpN).plateNum;
if prevExp==0
FexpScanSpots=Exp(expN).Dexp(DexpN).FexpScanSpots;
FexpScanBMtp=Exp(expN).Dexp(DexpN).FexpScanBMtp;
anlZoneRefs=Exp(expN).Dexp(DexpN).anlZoneRefs;
ImParMat=Exp(expN).Dexp(DexpN).ImParMat;
else
% check if the request expJob is already loaded in one of the other zones
matchfound=0;
for j=1:3
if isequal(expDir, char(fullfile(Exp(j).ExpFoldr)))
@@ -67,142 +59,130 @@ else
end
end
if matchfound==0
%if not, load data for previous experiment again.
% if not, load data for previous experiment again.
load(fullfile(char(OLresDir),'Fotos','Coordinates'))
load(fullfile(char(OLresDir),'Fotos','anlZones'))
load(fullfile(char(OLresDir),'Fotos','BGatTpts'))
load(fullfile(char(OLresDir),'PTmats','NImParameters'))
end %if matchfound==1
end %if prevExp==0
end
end
% Parameter Entry
width=ImParMat(5);
widthEx=width-1; %width extention from reference point
%**************Parameter Entry******************
width=ImParMat(5);
widthEx=width-1; %width extention from reference point
% Start Spot selection and Manipulation section
Fcutsc=[];
Fstrip=[];
%{
cd(fullfile(char(OLresDir)))
cd ..
expDir=pwd;
cd(w)
%}
%=================================================================
%=================================================================
%++++Start Spot selection and Manipulation section+++++++++++
Fcutsc=[];
Fstrip=[];
%{
cd(fullfile(char(OLresDir)))
cd ..
expDir=pwd;
cd(w)
%}
%tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
tPtsSize=size(FexpScanBMtp{1,plateNum},(3)); %tPtsSize=size(FexpScanBMtp{1,1},(3)); 20160110
%bmpFileLst=dirfullfile(char(OLresDir),num2str(plateNum),'*.bmp')); %(fullfile(expDir, char(ScLst(ScLstCnt)), '*.bmp'));
hsafety=figure;
dc= get(datacursormode)
imInterval=1;
try, imInterval= str2double(Exp(4).SpotVintervPar),catch,end
try
for tPt=1:imInterval:tPtsSize %tPtLength
coord=[];
% tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
tPtsSize=size(FexpScanBMtp{1,plateNum},(3)); % tPtsSize=size(FexpScanBMtp{1,1},(3)); 20160110
%bmpFileLst=dirfullfile(char(OLresDir),num2str(plateNum),'*.bmp')); %(fullfile(expDir, char(ScLst(ScLstCnt)), '*.bmp'));
hsafety=figure;
dc=get(datacursormode)
imInterval=1;
try,imInterval=str2double(Exp(4).SpotVintervPar),catch,end
try
%FtifFile= fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat(num2str(tPt),'.bmp')); %char(tifFileLst(tPt));
FtifFile= fullfile(char(expDir),num2str(plateNum),strcat(num2str(tPt),'.bmp'));
Fimg= imread(FtifFile);
% For Visualization Purposes ***********************
Fram= ones(2075,1400); %(size(Empsc,1),size(Empsc,2));
%FRAME ANALYSIS AREA*******************************************************
if size(FexpScanSpots,2)>1
for tPt=1:imInterval:tPtsSize %tPtLength
coord=[];
try
% FtifFile=fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum),strcat(num2str(tPt),'.bmp')); %char(tifFileLst(tPt));
FtifFile=fullfile(char(expDir),num2str(plateNum),strcat(num2str(tPt),'.bmp'));
Fimg=imread(FtifFile);
% For Visualization Purposes
Fram=ones(2075,1400); %(size(Empsc,1),size(Empsc,2));
% FRAME ANALYSIS AREA
if size(FexpScanSpots,2)>1
coord=FexpScanSpots{plateNum}{rIm,cIm,tPt};
else
else
coord=FexpScanSpots{plateNum,1,1}{rIm,cIm,tPt};
end
if size(anlZoneRefs,2)>1
end
if size(anlZoneRefs,2)>1
xyLoc=anlZoneRefs{plateNum}{rIm,cIm,tPt}; %F_Snum
else
else
xyLoc=anlZoneRefs{F_Snum,1,1}{rIm,cIm,tPt};
end
xLoc= xyLoc(2);
yLoc= xyLoc(1);
end
xLoc=xyLoc(2);
yLoc=xyLoc(1);
%*************CIRCLE related*************************
doCircle=1; %Temp test value insertion to get square images
if doCircle==1,
Fram= FoptCirMask;
else
%1->2 across rt 1, 2-4
Fram(yLoc,xLoc:(xLoc+widthEx))=0.8;
%1->4 down lf 1-3, 2
Fram((yLoc+1):(yLoc+1+widthEx),xLoc)=0.8;
%2->3 down rt 1-3, 4
Fram(yLoc:(yLoc+widthEx),(xLoc+1+widthEx))=0.8;
%4->3 Bot Across rt 1, 2-4
Fram((yLoc+1+widthEx),(xLoc+1):(xLoc+1+widthEx))=0.8;
Fram= Fram(coord(1):coord(3),coord(2):coord(4));
end
%CUT SPOT OUT OF IMAGE*****************************************************
%Fbg= FexpScanBMtp{selScan,1}(rIm,cIm,tPt);
Fbg= FexpScanBMtp{plateNum}(rIm,cIm,tPt); %{selScan,1}
%Fimg= imread(FtifFile); %,'PixelRegion', {[coord(1),coord(3)],[coord(2),coord(4)]});
Fcutsc= Fimg(coord(1):coord(3),coord(2):coord(4));
if doCircle==1
% CIRCLE related
doCircle=1; % temp test value insertion to get square images
if doCircle==1
Fram=FoptCirMask;
else
% 1->2 across rt 1, 2-4
Fram(yLoc,xLoc:(xLoc+widthEx))=0.8;
% 1->4 down lf 1-3, 2
Fram((yLoc+1):(yLoc+1+widthEx),xLoc)=0.8;
% 2->3 down rt 1-3, 4
Fram(yLoc:(yLoc+widthEx),(xLoc+1+widthEx))=0.8;
% 4->3 Bot Across rt 1, 2-4
Fram((yLoc+1+widthEx),(xLoc+1):(xLoc+1+widthEx))=0.8;
Fram=Fram(coord(1):coord(3),coord(2):coord(4));
end
% Cut Spot Out Of Image
% Fbg=FexpScanBMtp{selScan,1}(rIm,cIm,tPt);
Fbg=FexpScanBMtp{plateNum}(rIm,cIm,tPt); %{selScan,1}
% Fimg=imread(FtifFile); %,'PixelRegion', {[coord(1),coord(3)],[coord(2),coord(4)]});
Fcutsc=Fimg(coord(1):coord(3),coord(2):coord(4));
if doCircle==1
%varExt=size(Fcutsc)-size(Fram);
varExtPre= [((yLoc-0)-coord(1)) ((xLoc-0)-coord(2))];
varExtPost= [(coord(3)-(yLoc+diaExt+1)) (coord(4)-(xLoc+diaExt+1))];
varExtPre=[((yLoc-0)-coord(1)) ((xLoc-0)-coord(2))];
varExtPost=[(coord(3)-(yLoc+diaExt+1)) (coord(4)-(xLoc+diaExt+1))];
% Fram=padarray(Fram,[expansion expansion],1,'pre');
Fram=padarray(Fram,[varExtPre],1,'pre');
Fram=padarray(Fram,[varExtPost],1,'post');
%Fram=padarray(Fram,rem(varExt,2),1,'post');
% Fram=padarray(Fram,rem(varExt,2),1,'post');
%Fram=padarray(Fram,floor((varExt-2)./2),1);
end
%INVERT IMGAGE
Fcutsc=double(Fcutsc) .* Fram;
%Fcutsc= Fcutsc .* uint8(Fram);
Fcutsc=uint8(Fcutsc);
%Fcutsc=255 - (Fcutsc-Fbg);
Fcutsc=(Fcutsc-Fbg);
%Time series annotation**************************
tmPtTx=[];
tenths=(round(10*(Exp(expN).Dexp(DexpN).scan(plateNum).plate(1).tSeries(tPt)))) ./10;
tmPtTx= strcat(num2str(tenths),'h');
end
% Invert Image
Fcutsc=double(Fcutsc) .* Fram;
%Fcutsc=Fcutsc .* uint8(Fram);
Fcutsc=uint8(Fcutsc);
%Fcutsc=255 - (Fcutsc-Fbg);
Fcutsc=(Fcutsc-Fbg);
%Time series annotation**************************
tmPtTx=[];
tenths=(round(10*(Exp(expN).Dexp(DexpN).scan(plateNum).plate(1).tSeries(tPt)))) ./10;
tmPtTx=strcat(num2str(tenths),'h');
%imwrite(Fcutsc,(fullfile(resDir,'Fotos',strcat('FScan',num2str(selScan),'_timePt-',num2str(tPt),'.jpg'))),'jpg');
aCnt=aCnt+1;
if aCnt==1 %||tPt==1
% imwrite(Fcutsc,(fullfile(resDir,'Fotos',strcat('FScan',num2str(selScan),'_timePt-',num2str(tPt),'.jpg'))),'jpg');
aCnt=aCnt+1;
if aCnt==1 %||tPt==1
EZvapendLabel
Fstrip= vertcat(Fcutsc,Bspace);
Hspace= zeros(size(Fstrip,1),4)+1200; %+255
Fstrip= horzcat(Fstrip,Hspace);
end
makeVis=1;
if aCnt>1
Fstrip=vertcat(Fcutsc,Bspace);
Hspace=zeros(size(Fstrip,1),4)+1200; %+255
Fstrip=horzcat(Fstrip,Hspace);
end
makeVis=1;
if aCnt>1
EZvapendLabel
vcat= vertcat(Fcutsc,Bspace);
%Hspace= zeros(size(Fstrip,1),4)+255;
Fstrip= horzcat(Fstrip,vcat,Hspace);
end
% For Visualization Purposes only
vcat=vertcat(Fcutsc,Bspace);
%Hspace=zeros(size(Fstrip,1),4)+255;
Fstrip=horzcat(Fstrip,vcat,Hspace);
end
if makeVis==1
%if aCnt==1,figure;end
%resIm= uint8((double(BGsc) + OptmapOnesDbl) .* double(fullsc));
%clear('OptmapOnesDbl')
% For Visualization Purposes only
if makeVis==1
% if aCnt==1,figure;end
% resIm=uint8((double(BGsc) + OptmapOnesDbl) .* double(fullsc));
% clear('OptmapOnesDbl')
hfstrip=imagesc(Fcutsc); colormap(gray); %hfstrip=imshow(Fcutsc); colormap(gray); %hfscanIm=imagesc(Fcutsc); colormap(gray);
ghandles.hfstrip=gcf;
haxis=gca;
title(strcat('Scan',num2str(plateNum),'->timePt-',num2str(tPt)));
clf(hfstrip,'reset'); colormap(gray); %clf(hfscanIm,'reset'); colormap(gray);
set(ghandles.hfstrip,'NumberTitle','off')
end
end
expLabel=strcat('->',char(fullfile(char(OLresDir),num2str(OLplateNum))))
%catch
% catch
% expLabel=strcat('->',char(fullfile(Exp(expN).Dexp(DexpN).ExpFoldr,num2str(plateNum))))
if expN==1
set(ghandles.hfstrip,'Name', strcat(char(get(ghandles.OLay1,'string')),expLabel)) %ghandles.hfIm %{'ExpOutmat'} %strcat('EASYconsole- ',char(resDir)))
elseif expN==2
@@ -210,36 +190,31 @@ end
elseif expN==3
set(ghandles.hfstrip,'Name', strcat(char(get(ghandles.OLay3,'string')),expLabel))
end
%hgsave(fullfile(resDir,'Fotos',strcat('FScan',num2str(selScan),'_timePt-',num2str(tPt))));
catch
end
end %for tPt=1:tPtsSize end of for Fotos Spot image cutout
catch
end
%figure(ghandles.hFstrip)
imshow(Fstrip);
%{
%if tPt==tPtLength %length(tifFileLst)
catch
end
end
catch
end
%figure(ghandles.hFstrip)
imshow(Fstrip);
%{
%if tPt==tPtLength %length(tifFileLst)
%imwrite(Fstrip,(fullfile(resDir,'Fotos',strcat('Fstrip','S',num2str(selScan),'P',num2str(F_Pnum),'r',num2str(F_Rusrnum),'c',num2str(F_Cusrnum),'.jpg'))),'jpg');
F_name= strcat(fnamemod,'_Fstrip','.jpg');
F_name=strcat(fnamemod,'_Fstrip','.jpg');
%dfname=(fullfile(resDir,'Fotos',char(F_name)));
%delete(dfname); % imwrite nolonger overwrites ??why 14_0729
imwrite(Fstrip,(fullfile(resDir,'Fotos',char(F_name))),'jpg','Quality',100);
F_name= strcat(fnamemod,'_Fstrip','.tif');
F_name=strcat(fnamemod,'_Fstrip','.tif');
%dfname=(fullfile(resDir,'Fotos',char(F_name)));
%delete(dfname); % imwrite nolonger overwrites ??why
imwrite(Fstrip,(fullfile(resDir,'Fotos',char(F_name))),'tif');
%end
%}
%[output_txt]=datatipp(obj,event_obj);
%datacursormode off;
%datacursormode on;
%close(figure(hsafety))
end %function end
%XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
%XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
%XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
%end
%}
%[output_txt]=datatipp(obj,event_obj);
%datacursormode off;
%datacursormode on;
%close(figure(hsafety))
end

284
workflow/apps/matlab/ezview/EZusrSelRefx.m
View File

@@ -1,27 +1,27 @@
%EZusrSelRef
%User Select Reference Diaglog Box
% User Select Reference Diaglog Box
try
if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
%{
prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
'Enter GeneName of Your Reference:'};
rfMPstr= cell2mat(answer(1));
rfMPstr=cell2mat(answer(1));
rfMPcomas=strfind((cell2mat(answer(1))),',');
n=0;
if isempty(rfMPcomas)|| max(rfMPcomas)== length(rfMPstr)
usrMPs= rfMPstr
if isempty(rfMPcomas)|| max(rfMPcomas)==length(rfMPstr)
usrMPs=rfMPstr
else
for i= rfMPcomas,
for i=rfMPcomas,
n=n+1
usrMPs(n)= str2double(rfMPstr(i-1:i))
if i== max(rfMPcomas)
usrMPs(n+1)= str2double(rfMPstr(i:end))
usrMPs(n)=str2double(rfMPstr(i-1:i))
if i==max(rfMPcomas)
usrMPs(n+1)=str2double(rfMPstr(i:end))
end
end
end
usrMPs= answer(1);
refGene= answer(2);
usrMPs=answer(1);
refGene=answer(2);
%}
prompt={'Enter GeneName to use as Reference:',...
'Enter Specifics Term if used to futher specify Reference '}
@@ -29,195 +29,171 @@ if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
num_lines=1;
def={'None','Specifics Term'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
rfGenestr= cell2mat(answer(1));
rfSpec= cell2mat(answer(2));
rfGenestr=cell2mat(answer(1));
rfSpec=cell2mat(answer(2));
end
end
%try
for mp=1:length(Exp(expN).Dexp(DexpN).MP)
%try
for mp=1:length(Exp(expN).Dexp(DexpN).MP)
for ind384=1:384
spN=spN+1;
end
%catch
%end %try for user selected Reference routine
end
%catch
%end %try for user selected Reference routine
end
%***********DISPERSE REFERENCE PLATES
Exp(expN).Dexp(DexpN).RFmdPindx=[];
Exp(expN).Dexp(DexpN).RFmdPpltN=[];
if exist('drf','var') %('RF1scanN','var')
%Det. index of change from one MP to the next
% Disperse Reference Plates
Exp(expN).Dexp(DexpN).RFmdPindx=[];
Exp(expN).Dexp(DexpN).RFmdPpltN=[];
if exist('drf','var') % ('RF1scanN','var')
%Det. index of change from one MP to the next
i=2;
chgIndx(1)=1;
for j=1:length(drf(:,3))
for j=1:length(drf(:,3))
if j>1
if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
if cell2mat(drf(j,3))~=cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
end
end
chgIndx(length(chgIndx)+1)= length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)= cell2mat(drf(:,3:6))
vv= zeros(length(drf),DMnum);
%************************************
dMPs= unique(cell2mat(drf(:,3)));
%*****************************************
end
chgIndx(length(chgIndx)+1)=length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)=cell2mat(drf(:,3:6))
vv=zeros(length(drf),DMnum);
dMPs=unique(cell2mat(drf(:,3)));
%{
for mm=1:MPnum
nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
end
%}
%nzValsG= zeros(DMnum,size(drf,1));
%nzValsAcc= zeros(DMnum,384);
% nzValsG=zeros(DMnum,size(drf,1));
% nzValsAcc=zeros(DMnum,384);
for mm=1:length(dMPs) % length(chgIndx)
for d=1:(DMnum)
medianIndxDisp=[];
NZrefIndxP=[];
nonZeroValsP=[];
medValLstDisp=[];
rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
try % Determine the dispersed RFs median mean and std if such exist
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
%vv= Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
try % Determine the dispersed RFs median mean and std if such exist
NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
% vv=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
nonZeroValsP= nonzeros(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp= std(nonZeroValsP);
mean1Disp= mean(nonZeroValsP);
minDisp= min(nonZeroValsP);
maxDisp= max(nonZeroValsP);
nonZeroValsP=nonzeros(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp=std(nonZeroValsP);
mean1Disp=mean(nonZeroValsP);
minDisp=min(nonZeroValsP);
maxDisp=max(nonZeroValsP);
drfVals=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
%nzValsAcc(mm).DM(d,:)= nonZeroValsP;
%nzValsAcc(mm).DM(d,:)=nonZeroValsP;
%MEDIAN Determination for PLATES with Dispersed RFs
%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP;
else nonZeroCntDisp=length(NZrefIndxP);
%NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
if isempty(NZrefIndxP)
nonZeroCntDisp=0
medianIndxDisp=NZrefIndxP;
else
nonZeroCntDisp=length(NZrefIndxP);
end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp= NZrefIndxP(1:nonZeroCntDisp-1); end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLstDisp= Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
%medValList1Disp{d}= medValLstDisp;
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp=NZrefIndxP(1:nonZeroCntDisp-1); end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp=NZrefIndxP; end
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLstDisp=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
%medValList1Disp{d}=medValLstDisp;
mval1Disp=median(medValLstDisp); %mval1=median(Exp(expN).Dexp(DexpN).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); %(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))); %(nonZeroIndxDisp,5))); %((nonZrfIndx.mp{dMPs(mm),:}),5)));
RFmd1posD= NZrefIndxP(nonZeroMedPosIndx); %drfPindx((RFmd1posIndx),dMPs(mm));
RFmd1locD(1)= ceil(RFmd1posD/24); %calc r value
RFmd1locD(2)= RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1mdP(',num2str(d),')')};
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
bb(lstindxOrf,1)= {strcat('RF1mdP(',num2str(d),')')};
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
Exp(expN).Dexp(DexpN).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))= RFmd1posD;
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(DexpN).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
Exp(expN).Dexp(DexpN).RFmedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(DexpN).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(DexpN).meanP(d,dMPs(mm))= mean1Disp;
Exp(expN).Dexp(DexpN).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(DexpN).maxP(d,dMPs(mm))= maxDisp;
else
RFmd1posD=NZrefIndxP(nonZeroMedPosIndx); %drfPindx((RFmd1posIndx),dMPs(mm));
RFmd1locD(1)=ceil(RFmd1posD/24); %calc r value
RFmd1locD(2)=RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf=lstindxOrf+1;
aa(lstindx,1)={strcat('RF1mdP(',num2str(d),')')};
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
bb(lstindxOrf,1)={strcat('RF1mdP(',num2str(d),')')};
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
Exp(expN).Dexp(DexpN).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=RFmd1posD;
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(DexpN).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
Exp(expN).Dexp(DexpN).RFmedianP(d,dMPs(mm))=mval1Disp;
Exp(expN).Dexp(DexpN).stdP(d,dMPs(mm))=std1Disp;
Exp(expN).Dexp(DexpN).meanP(d,dMPs(mm))=mean1Disp;
Exp(expN).Dexp(DexpN).minP(d,dMPs(mm))=minDisp;
Exp(expN).Dexp(DexpN).maxP(d,dMPs(mm))=maxDisp;
else
% Need to set L r K values to zeros or pick the first spot with zeros
%Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection'
firstZeroDindx= find(((Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
% Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
medianCalcFailedD='To Few nonZero spots for valid median RF1 selection'
firstZeroDindx=find(((Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroD;
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
end %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 ln584
catch %try ln565
medianCalcTryFailed1D= 'Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
try
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx= uu(firstZeroindxD,4);
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
end
catch
catchissue='try at Ln565'
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
medianCalcTryFailed1D='Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
try
firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx=uu(firstZeroindxD,4);
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
catch
Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(DexpN).RFmdPpltN= dMPs(mm);
Exp(expN).Dexp(DexpN).RFmdPpltN=dMPs(mm);
catch
catchissue='Ln619'
Exp(expN).Dexp(DexpN).RFmdPpltN= 1; %This might keep from breaking BUT ???
Exp(expN).Dexp(DexpN).RFmdPpltN=1; %This might keep from breaking BUT ???
end
error='EZexpSel lineAfter 565'
end %try ~ln565
end
end % for d=0:DMnum
end % for mm=1:length(dMPs)
end %for d=0:DMnum
end %for mm=1:length(dMPs)
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
uu= horzcat(uu,vv);
for d=1:DMnum
% Calc. Global Mean, Std, And Median For Distributed References
uu=horzcat(uu,vv);
for d=1:DMnum
medianIndxG=[];
NZrfIndxG=[];
minG=min(nonzeros(vv(:,d)));
maxG=max(nonzeros(vv(:,d)));
RFmeanG= mean(nonzeros(vv(:,d)));
RFstdG= std(nonzeros(vv(:,d)));
NZrfIndxG= find(nonzeros(vv(:,d)));
RFmeanG=mean(nonzeros(vv(:,d)));
RFstdG=std(nonzeros(vv(:,d)));
NZrfIndxG=find(nonzeros(vv(:,d)));
if isempty(RFmeanG), nonZeroCntD=0, %medianIndxDisp= RFmeanG(d);
else nonZeroCntD= length(nonzeros(vv(:,d)));
if isempty(RFmeanG)
nonZeroCntD=0
% medianIndxDisp=RFmeanG(d);
else
nonZeroCntD=length(nonzeros(vv(:,d)));
end
%Calc. of median requires an odd number of indx items
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD= NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD= NZrfIndxG(:); end
if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
mvalsDG= median(vv(medianIndxD,d)); %(nonzeros(vv(:,d)));
% Calc. of median requires an odd number of indx items
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD=NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD=NZrfIndxG(:); end
if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) % To calc. a median, more than 15% of spots must be nonZero
mvalsDG=median(vv(medianIndxD,d)); % (nonzeros(vv(:,d)));
nzPosIndxDG=find(mvalsDG==vv(:,d));
RFmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
RFmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
RFmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1mdG(',num2str(d),')')};
aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)= {strcat('RF1mdG(',num2str(d),')')};
bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
Exp(expN).Dexp(DexpN).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(DexpN).RFmdGindx(d)= nzPosIndxDG;
Exp(expN).Dexp(DexpN).RFmdGpltN(d)= RFmdDGloc(d,1);
Exp(expN).Dexp(DexpN).RFmdGscanN(d)= uu(nzPosIndxDG,4);
Exp(expN).Dexp(DexpN).RFmedianG(d)= mvalsDG;
Exp(expN).Dexp(DexpN).RFminG(d)= minG;
Exp(expN).Dexp(DexpN).RFmaxG(d)= maxG;
Exp(expN).Dexp(DexpN).RFstdG(d)= RFstdG;
Exp(expN).Dexp(DexpN).RFmeanG(d)= RFmeanG;
RFmdDGloc(d,1)=uu(nzPosIndxDG,1); % MP of distributedGlobal Median value
RFmdDGloc(d,2)=uu(nzPosIndxDG,2); % calc r value
RFmdDGloc(d,3)=uu(nzPosIndxDG,3); % calc c value
lstindx=lstindx+1;
lstindxOrf=lstindxOrf+1;
aa(lstindx,1)={strcat('RF1mdG(',num2str(d),')')};
aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)={strcat('RF1mdG(',num2str(d),')')};
bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
Exp(expN).Dexp(DexpN).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(DexpN).RFmdGindx(d)=nzPosIndxDG;
Exp(expN).Dexp(DexpN).RFmdGpltN(d)=RFmdDGloc(d,1);
Exp(expN).Dexp(DexpN).RFmdGscanN(d)=uu(nzPosIndxDG,4);
Exp(expN).Dexp(DexpN).RFmedianG(d)=mvalsDG;
Exp(expN).Dexp(DexpN).RFminG(d)=minG;
Exp(expN).Dexp(DexpN).RFmaxG(d)=maxG;
Exp(expN).Dexp(DexpN).RFstdG(d)=RFstdG;
Exp(expN).Dexp(DexpN).RFmeanG(d)=RFmeanG;
end
end
end
catch
msg='Failed attempt to apply User Selected Reference'
end
end % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
%*********************************************************************
catch
msg= 'Failed attempt to apply User Selected Reference'
end %if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var')

578
workflow/apps/matlab/ezview/EZvDatatip.m
View File

@@ -1,5 +1,5 @@
%EZvDatatip 230802 attempting to fix for R2023a
%Calls to EZdestComp.m EZmDayTrend.m
% EZvDatatip 230802 attempting to fix for R2023a
% Calls to EZdestComp.m EZmDayTrend.m
global ghandles
global Exp
@@ -7,99 +7,88 @@ global zonePB
RFcmpGFlg=0; %Test 180105 as it goes to EZmDayTrend.m
lstBoxCmpFlg=0;
curKey=get(gcf,'currentkey')
htMapFg=0;
curKey=get(gcf,'currentkey')
htMapFg=0;
if ghandles.Iaxes1==get(htargetAxes,'Parent'),expN=1;
elseif ghandles.Iaxes2==get(htargetAxes,'Parent'),expN=2;
elseif ghandles.Iaxes3==get(htargetAxes,'Parent'),expN=3;
elseif ghandles.OLaxes1==get(htargetAxes,'Parent'),OLay=1; expN=1; %zone=1; datacursormode off;
elseif ghandles.OLaxes2==get(htargetAxes,'Parent'),OLay=2; expN=2; %zone=2; datacursormode off;
elseif ghandles.OLaxes3==get(htargetAxes,'Parent'),OLay=3; expN=3; %zone=3; datacursormode off;
elseif ghandles.HtMap1==get(htargetAxes,'Parent'),expN=1; htMapFg=1;
elseif ghandles.HtMap2==get(htargetAxes,'Parent'),expN=2; htMapFg=1;
elseif ghandles.HtMap3==get(htargetAxes,'Parent'),expN=3; htMapFg=1;
else
if ghandles.Iaxes1==get(htargetAxes,'Parent'),expN=1;
elseif ghandles.Iaxes2==get(htargetAxes,'Parent'),expN=2;
elseif ghandles.Iaxes3==get(htargetAxes,'Parent'),expN=3;
elseif ghandles.OLaxes1==get(htargetAxes,'Parent'),OLay=1; expN=1; %zone=1; datacursormode off;
elseif ghandles.OLaxes2==get(htargetAxes,'Parent'),OLay=2; expN=2; %zone=2; datacursormode off;
elseif ghandles.OLaxes3==get(htargetAxes,'Parent'),OLay=3; expN=3; %zone=3; datacursormode off;
elseif ghandles.HtMap1==get(htargetAxes,'Parent'),expN=1; htMapFg=1;
elseif ghandles.HtMap2==get(htargetAxes,'Parent'),expN=2; htMapFg=1;
elseif ghandles.HtMap3==get(htargetAxes,'Parent'),expN=3; htMapFg=1;
else
return
end
end
if expN==1,DexpN= (get(ghandles.DN1,'value')); end
if expN==2,DexpN= (get(ghandles.DN2,'value')); end
if expN==3,DexpN= (get(ghandles.DN3,'value')); end
if expN==1,DexpN=(get(ghandles.DN1,'value')); end
if expN==2,DexpN=(get(ghandles.DN2,'value')); end
if expN==3,DexpN=(get(ghandles.DN3,'value')); end
% Exp(expN).DexpN=DexpN;
% Exp(expN).DexpN=DexpN;
if strcmp(Exp(expN).DexpType,'single'), DexpN=1; end
if exist('OLay','var'), clear ExpN; end
if ~exist('OLay','var')
try
try
ImageSel=expN<4
destPerMP= Exp(expN).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
destPerMP=Exp(expN).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
MPsel=Exp(expN).Dexp(DexpN).MPsel; %floor(get(handles.MPsldr1,'value'));
pertSel=Exp(expN).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
tPtSel=Exp(expN).Dexp(DexpN).tPtSel; %floor(get(handles.Tptsldr1,'value'));
plateNum= Exp(expN).Dexp(DexpN).plateNum; %(MPsel1-1)*destPerMP1 + pertSel1;
scan= Exp(expN).Dexp(DexpN).scan;
plateNum=Exp(expN).Dexp(DexpN).plateNum; %(MPsel1-1)*destPerMP1 + pertSel1;
scan=Exp(expN).Dexp(DexpN).scan;
MP=Exp(expN).Dexp(DexpN).MP;
ptrPos=[cpos(1),cpos(2)]; %for VerticleImage
if htMapFg==0 %Comes from spot image Iaxes
try
for m=1:24
for n=1:16
coord=Exp(expN).Dexp(DexpN).FexpScanSpots{plateNum}{m,n,tPtSel}; %replace {1} with {plateNum}
if ptrPos(2)> coord(1) && ptrPos(2)< coord(3)
if ptrPos(1)> coord(2) && ptrPos(1)<coord(4)
picLoc1= [n,m];
spotFrm= Exp(expN).Dexp(DexpN).FexpScanSpots{plateNum}{m,n,tPtSel}; %20160108
picLoc1=[n,m];
spotFrm=Exp(expN).Dexp(DexpN).FexpScanSpots{plateNum}{m,n,tPtSel}; %20160108
end
end
end %for n=1:16
end %for m=1:24
destcompMsg= 'GoodDataTip';
end
end
destcompMsg='GoodDataTip';
catch
destcompMsg= 'BadDataTip';
destcompMsg='BadDataTip';
m
n
end
plateLoc= [(17-picLoc1(1)) picLoc1(2)];
plateLoc=[(17-picLoc1(1)) picLoc1(2)];
indx=(plateLoc(1)-1)*24+plateLoc(2);
elseif htMapFg==1 %Comes from HeatMap image Haxes
plateLoc= ptrPos;
plateLoc=ptrPos;
indx=(plateLoc(1)-1)*24+plateLoc(2);
end
Exp(expN).Dexp(DexpN).spotIndx=indx;
K=scan(1,plateNum).plate(1).CFout(indx,3); Ks=num2str(K);
r=scan(1,plateNum).plate(1).CFout(indx,4); rs=num2str(r);
l=scan(1,plateNum).plate(1).CFout(indx,5); Ls=num2str(l);
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
Kl=scan(1,plateNum).plate(1).CFout(indx,7);
Ku=scan(1,plateNum).plate(1).CFout(indx,8);
rl=scan(1,plateNum).plate(1).CFout(indx,9);
ru=scan(1,plateNum).plate(1).CFout(indx,10);
lfast=scan(1,plateNum).plate(1).CFout(indx,11);
lslow=scan(1,plateNum).plate(1).CFout(indx,12);
t=1:200;
clear g;
K=scan(1,plateNum).plate(1).CFout(indx,3); Ks= num2str(K);
r=scan(1,plateNum).plate(1).CFout(indx,4); rs= num2str(r);
l=scan(1,plateNum).plate(1).CFout(indx,5); Ls= num2str(l);
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
Kl=scan(1,plateNum).plate(1).CFout(indx,7);
Ku=scan(1,plateNum).plate(1).CFout(indx,8);
rl=scan(1,plateNum).plate(1).CFout(indx,9);
ru=scan(1,plateNum).plate(1).CFout(indx,10);
lfast=scan(1,plateNum).plate(1).CFout(indx,11);
lslow=scan(1,plateNum).plate(1).CFout(indx,12);
t=1:200;
clear g;
try
g= K ./ (1 + exp(-r.* (t - l )));
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
tser=(scan(1,plateNum).plate(1).t0Series(:));
rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
try
g=K ./ (1 + exp(-r.* (t - l )));
gSlow=Kl ./ (1 + exp(-rl.* (t - lslow )));
gFast=Ku ./ (1 + exp(-ru.* (t - lfast )));
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
tser=(scan(1,plateNum).plate(1).t0Series(:));
rawData=scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
if expN==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
Exp(1).traceN=Exp(1).traceN+1;
traceN=Exp(1).traceN;
@@ -112,83 +101,75 @@ rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(i
Exp(3).traceN=Exp(3).traceN+1;
traceN=Exp(3).traceN;
end
plot(plotAxes,t,g);hold(plotAxes,'on');
plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,g);hold(plotAxes,'on');
plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');
hold(plotAxes,'off');
try for i=1:length(Exp(expN).hOL(:)),set(Exp(expN).hOL(i),'color',[0 0 1]); end, catch, end %ZoneRelated
try
for i=1:length(Exp(expN).hOL(:)),set(Exp(expN).hOL(i),'color',[0 0 1]); end, catch, end %ZoneRelated
if verLessThan('matlab','8.4')
else %accomodate new matlab changes after 2014a fix 23_0807
tempFig= figure;
else % accomodate new matlab changes after 2014a fix 23_0807
tempFig=figure;
end
Exp(expN).hOL(traceN)=plot(OLaxes,t,g);hold on;
Exp(expN).hOL(traceN)=plot(OLaxes,t,g);hold on;
set(Exp(expN).hOL(traceN),'color',[1 0 0])
Exp(expN).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*');
% Added for Composite Plot utility [C] 170419
Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
set(Exp(expN).hOL(traceN),'color',[1 0 0])
Exp(expN).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*');
%Added for Composite Plot utility [C] 170419
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
%************************************************
if verLessThan('matlab','8.4')
else %accomodate new matlab changes after 2014a fix update 23_0807
if verLessThan('matlab','8.4')
else % accomodate new matlab changes after 2014a fix update 23_0807
close(tempFig)
end
catch
end
catch
%{
g= K ./ (1 + exp(-r.* (t - l )));
g=K ./ (1 + exp(-r.* (t - l )));
if K==0||r==0||l==0, g(1:200)=1;end
tser=(scan(1,plateNum).plate(1).t0Series(:));
rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
rawData=scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
plot(plotAxes, plot(t,g),hold on,plot(tser,rawData,'g*'),hold off);
plot(OLaxes, plot(t,g),hold on,plot(tser,rawData,'g*');
%}
end %trycatch
%Get the DM agar description
if expN==1,DMstr=char(get(ghandles.DM1,'string'));end
if expN==2,DMstr=char(get(ghandles.DM2,'string'));end
if expN==3,DMstr=char(get(ghandles.DM3,'string'));end
end
% Get the DM agar description
if expN==1,DMstr=char(get(ghandles.DM1,'string'));end
if expN==2,DMstr=char(get(ghandles.DM2,'string'));end
if expN==3,DMstr=char(get(ghandles.DM3,'string'));end
gene=MP(1,MPsel).genename{1,1}(indx); orf=MP(1,MPsel).orf{1,1}(indx);
spec=MP(1,MPsel).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
geneOrfstr= strcat(gene,'_',orf,'_','r',num2str(plateLoc(1)),'c',num2str(plateLoc(2)),'_',tPtStr);
grfgenestr= strcat(gene,'_',orf,'_','r',num2str(plateLoc(1)),'c',num2str(plateLoc(2)));
selGnOrf= grfgenestr; %added for EZdestComp.m and EZmDayTrend.m
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(expN).Dexp(DexpN).resDir);
if ispc,
gene=MP(1,MPsel).genename{1,1}(indx); orf=MP(1,MPsel).orf{1,1}(indx);
spec=MP(1,MPsel).specifics{1,1}(indx); % orfrep=MP(1,plateNum).orfRep{1,1}(indx);
tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
geneOrfstr=strcat(gene,'_',orf,'_','r',num2str(plateLoc(1)),'c',num2str(plateLoc(2)),'_',tPtStr);
grfgenestr=strcat(gene,'_',orf,'_','r',num2str(plateLoc(1)),'c',num2str(plateLoc(2)));
selGnOrf=grfgenestr; % added for EZdestComp.m and EZmDayTrend.m
graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
spotDescrip=strcat(graphStr,'->',DMstr);
xp=char(Exp(expN).Dexp(DexpN).resDir);
if ispc,
slashPos=strfind(char(Exp(expN).Dexp(DexpN).resDir),'\');
else
else
slashPos=strfind(char(Exp(expN).Dexp(DexpN).resDir),'/');
end
end
startPos=slashPos(length(slashPos)-2) +1;
endPos=(slashPos(length(slashPos)) -1);
expStr= {xp(startPos:endPos)};
startPos=slashPos(length(slashPos)-2) +1;
endPos=(slashPos(length(slashPos)) -1);
expStr={xp(startPos:endPos)};
Exp(expN).hOLname(traceN)= spotDescrip; %ZoneRelated %graphStr; %ghandles.Exp(expN).hOLname(traceN)= graphStr;
Exp(expN).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(expN).hOLresDir(traceN)= {Exp(expN).Dexp(DexpN).resDir};
Exp(expN).hOLplateNum(traceN)= plateNum;
Exp(expN).hOLname(traceN)=spotDescrip; % ZoneRelated %graphStr; %ghandles.Exp(expN).hOLname(traceN)=graphStr;
Exp(expN).hOLexpNm(traceN)=expStr; % ghandles.Exp(expN).hOLexpNm(traceN)=expStr;
Exp(expN).hOLresDir(traceN)={Exp(expN).Dexp(DexpN).resDir};
Exp(expN).hOLplateNum(traceN)=plateNum;
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
% traceData=vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
if expN==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if expN==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if expN==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if expN==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end % graphStr);end % Displays the value.
if expN==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end % graphStr);end
if expN==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end % graphStr);end
if expN==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
if expN==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if expN==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if expN==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
if expN==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
if expN==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
%************************* ********************* ***************************
try
try
if expN==1, %&& get(ghandles.rotPB1,'value')~=1
try if length(char(Exp(expN).hOLname(traceN)))>40,set(ghandles.OLay1,'FontSize',8);end, catch end
set(ghandles.OLay1,'string', Exp(expN).hOLname(traceN));
@@ -207,12 +188,11 @@ try
try if length(char(Exp(expN).hOLexpNm(traceN)))>40,set(ghandles.OLexp3,'FontSize',8);end, catch end
set(ghandles.OLexp3,'string',Exp(expN).hOLexpNm(traceN));
end
catch
end
catch
end
%*******************************************************
%{
if expN==1
%{
if expN==1
zonesel=1;
set(ghandles.zoneRad1,'value',1)
set(ghandles.zoneRad2,'value',0)
@@ -223,9 +203,9 @@ if expN==1
else
set(ghandles.listboxGnOrf,'string',Exp(1).Dexp(DexpN).srtGnLst)
end
end
end
if expN==2
if expN==2
zonesel=2;
set(ghandles.zoneRad2,'value',1)
set(ghandles.zoneRad1,'value',0)
@@ -236,9 +216,9 @@ if expN==2
else
set(ghandles.listboxGnOrf,'string',Exp(2).Dexp(DexpN).srtGnLst)
end
end
end
if expN==3
if expN==3
zonesel=3;
set(ghandles.zoneRad3,'value',1)
set(ghandles.zoneRad2,'value',0)
@@ -249,13 +229,13 @@ if expN==3
else
set(ghandles.listboxGnOrf,'string',Exp(3).Dexp(DexpN).srtGnLst)
end
end
%}
%****************************************************************
%Zone PB set here as replacement for zonePB radio buttons 230815
if expN==1
end
%}
% Zone PB set here as replacement for zonePB radio buttons 230815
if expN==1
zonesel=1;
zonePB= expN;
zonePB=expN;
set(ghandles. zonePB1,'value',1)
set(ghandles. zonePB2,'value',0)
set(ghandles. zonePB3,'value',0)
@@ -268,11 +248,11 @@ if expN==1
else
set(ghandles.listboxGnOrf,'string',Exp(1).Dexp(DexpN).srtGnLst)
end
end
end
if expN==2
if expN==2
zonesel=2;
zonePB= expN;
zonePB=expN;
set(ghandles. zonePB2,'value',1)
set(ghandles. zonePB1,'value',0)
set(ghandles. zonePB3,'value',0)
@@ -285,11 +265,11 @@ if expN==2
else
set(ghandles.listboxGnOrf,'string',Exp(2).Dexp(DexpN).srtGnLst)
end
end
end
if expN==3
if expN==3
zonesel=3;
zonePB= expN;
zonePB=expN;
set(ghandles. zonePB3,'value',1)
set(ghandles. zonePB2,'value',0)
set(ghandles. zonePB1,'value',0)
@@ -302,138 +282,120 @@ if expN==3
else
set(ghandles.listboxGnOrf,'string',Exp(3).Dexp(DexpN).srtGnLst)
end
end
%***********************************************************************
end
Exp(expN).Trace(traceN).UsrGLB=geneOrfstr;
Exp(expN).Trace(traceN).dmSel=pertSel;
Exp(expN).Trace(traceN).DexpN=DexpN;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).UsrLvals=l;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).UsrKvals=K;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).Usrrvals=r;
catch
msg='NotImage'
end
end
% Write Selected Trace Info to OLAY header
try
OLayTest=OLay<4
msg='OLay'
% make all traces blue
for i=1:length(Exp(OLay).hOL(:))
try set(Exp(OLay).hOL(i),'color',[0 0 1]), catch end
end
Exp(expN).Trace(traceN).UsrGLB= geneOrfstr;
Exp(expN).Trace(traceN).dmSel= pertSel;
Exp(expN).Trace(traceN).DexpN= DexpN;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).UsrLvals= l;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).UsrKvals= K;
Exp(expN).Trace(traceN).Dexp(DexpN).DM(pertSel).Usrrvals= r;
%**************************************************************
catch
msg= 'NotImage'
end % trycatch expN<4 datatip selection from Image (not from an OverLay Plot)
end %if ~exist('OLay','var')
%******************************************************************************************
%Write Selected Trace Info to OLAY header********************+++++++++++++++++*************
try
OLayTest=OLay<4
msg='OLay'
%make all traces blue
for i=1:length(Exp(OLay).hOL(:))
try set(Exp(OLay).hOL(i),'color',[0 0 1]), catch end
end
%if get(ghandles.rotPB1,'value')~=1,
for i=1:length(Exp(OLay).hOL(:))
% if get(ghandles.rotPB1,'value')~=1,
for i=1:length(Exp(OLay).hOL(:))
htargetAxes
Exp(OLay).hOL(i)
if htargetAxes==Exp(OLay).hOL(i)
if htargetAxes==Exp(OLay).hOL(i)
if OLay==1 && get(ghandles.rotPB1,'value')~=1,
set(htargetAxes,'color',[1 0 0])
try if length(char(Exp(OLay).hOLname(i)))>40,set(ghandles.OLay1,'FontSize',8);end, catch, end
set(ghandles.OLay1,'string', Exp(OLay).hOLname(i));
traceLab= char(Exp(OLay).hOLname(i));
traceLab=char(Exp(OLay).hOLname(i));
try if length(char(Exp(OLay).hOLexpNm(i)))>40,set(ghandles.OLexp1,'FontSize',8);end, catch, end
set(ghandles.OLexp1,'string',Exp(OLay).hOLexpNm(i));
OLresDir= Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)= Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum= Exp(expN).Dexp(DexpN).plateNum
OLplateNum= Exp(OLay).hOLplateNum(i);
OLresDir=Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)=Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum=Exp(expN).Dexp(DexpN).plateNum
OLplateNum=Exp(OLay).hOLplateNum(i);
seltraceN=i;
end
if OLay==2 && get(ghandles.rotPB2,'value') ~=1
set(htargetAxes,'color',[1 0 0])
try if length(char(Exp(OLay).hOLname(i)))>40,set(ghandles.OLay2,'FontSize',8);end, catch, end
set(ghandles.OLay2,'string', Exp(OLay).hOLname(i));
traceLab= char(Exp(OLay).hOLname(i));
traceLab=char(Exp(OLay).hOLname(i));
try if length(char(Exp(OLay).hOLexpNm(i)))>40,set(ghandles.OLexp2,'FontSize',8);end, catch, end
set(ghandles.OLexp2,'string',Exp(OLay).hOLexpNm(i));
OLresDir= Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)= Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum= Exp(expN).Dexp(DexpN).plateNum
OLplateNum= Exp(OLay).hOLplateNum(i);
OLresDir=Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)=Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum=Exp(expN).Dexp(DexpN).plateNum
OLplateNum=Exp(OLay).hOLplateNum(i);
seltraceN=i;
end
if OLay==3 && get(ghandles.rotPB3,'value') ~=1
set(htargetAxes,'color',[1 0 0])
try if length(char(Exp(OLay).hOLname(i)))>40,set(ghandles.OLay3,'FontSize',8);end, catch, end
set(ghandles.OLay3,'string', Exp(OLay).hOLname(i));
traceLab= char(Exp(OLay).hOLname(i));
traceLab=char(Exp(OLay).hOLname(i));
try if length(char(Exp(OLay).hOLexpNm(i)))>40,set(ghandles.OLexp3,'FontSize',8);end, catch, end
set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(i));
OLresDir= Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)= Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum= Exp(expN).Dexp(DexpN).plateNum
OLplateNum= Exp(OLay).hOLplateNum(i);
OLresDir=Exp(OLay).hOLresDir(i);
Exp(OLay).hOLplateNum(i)=Exp(expN).Dexp(DexpN).plateNum %bug fix for OLay "chrono' RF_cmp( ) trend
plateNum=Exp(expN).Dexp(DexpN).plateNum
OLplateNum=Exp(OLay).hOLplateNum(i);
seltraceN=i;
end
Exp(OLay).seltraceN=seltraceN;
else
else
msg='Cant Find trace'
end
end
end
end % => for i=1:length(Exp(OLay).hOL(:))
%Extract row and col values from stored trace label for dest compare plots(EZdestComp)
%if a RFcmp_ is selected Need alternate method.
%if the Composite button is active, Need yet another method.
try
% Extract row and col values from stored trace label for dest compare plots(EZdestComp)
% if a RFcmp_ is selected Need alternate method.
% if the Composite button is active, Need yet another method.
try
tracename=char(Exp(OLay).hOLname(seltraceN))
pos_= strfind(tracename,'_')
rxcy= tracename(pos_(2):pos_(3))
cindx= strfind(rxcy,'c')
rindx= strfind(rxcy,'r')
LBr= str2num(rxcy((rindx+1):cindx-1))
LBc= str2num(tracename((pos_(2)+cindx): pos_(3)-1))
pos_=strfind(tracename,'_')
rxcy=tracename(pos_(2):pos_(3))
cindx=strfind(rxcy,'c')
rindx=strfind(rxcy,'r')
LBr=str2num(rxcy((rindx+1):cindx-1))
LBc=str2num(tracename((pos_(2)+cindx): pos_(3)-1))
indx=((LBr-1)*24) +LBc
grfgenestr= tracename(1:pos_(3)-1)
scan= Exp(OLay).Dexp(DexpN).scan;
grfgenestr=tracename(1:pos_(3)-1)
scan=Exp(OLay).Dexp(DexpN).scan;
EZdatatip=2;
try
tracename=char(Exp(OLay).hOLname(seltraceN))
EZdatatip=2;
catch
end
catch
catch
msg='Not from an OLay selected trace'
end
catch
msg='Not in OLay frame-axis 0'
end %=> try for Write Selected Trace Info to OLAY header******
%HIDE HIDE HIDE ---------------------------------------------------
%HIDE selected plot trace****rotPBx used for 'Hide'****************
try
OLayTest=OLay<4
end
catch
msg='Not in OLay frame-axis 0'
end
% Hide selected plot trace: rotPBx used for 'Hide'
try
OLayTest=OLay<4
msg='OLay'
OLay
if get(ghandles.rotPB1,'value') ==1 && OLay==1,
%make all traces blue
if get(ghandles.rotPB1,'value') ==1 && OLay==1,
% make all traces blue
for i=1:length(Exp(OLay).hOL(:))
set(Exp(OLay).hOL(i),'color',[0 0 1])
end
for i=1:length(Exp(OLay).hOL(:))
if htargetAxes==Exp(OLay).hOL(i)
hidAx1traceN=i
set(Exp(OLay).hOL(i),'Visible','off')
set(Exp(OLay).hOLb(i),'Visible','off')
for j=1:length(Exp(OLay).hOL(:))
if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN= j; end
if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN=j; end
end
end
if htargetAxes==Exp(OLay).hOL(i), break;end
@@ -443,17 +405,16 @@ if get(ghandles.rotPB1,'value') ==1 && OLay==1,
if OLay==1
try if length(char(Exp(OLay).hOLname(maxhN)))>40,set(ghandles.OLay1,'FontSize',8);end, catch, end
set(ghandles.OLay1,'string', Exp(OLay).hOLname(maxhN));
traceLab= char(Exp(OLay).hOLname(maxhN));
traceLab=char(Exp(OLay).hOLname(maxhN));
try if length(char(Exp(OLay).hOLexpNm(maxhN)))>40,set(ghandles.OLexp1,'FontSize',8);end, catch, end
set(ghandles.OLexp1,'string',Exp(OLay).hOLexpNm(maxhN));
OLresDir= Exp(OLay).hOLresDir(maxhN);
OLplateNum= Exp(OLay).hOLplateNum(maxhN);
OLresDir=Exp(OLay).hOLresDir(maxhN);
OLplateNum=Exp(OLay).hOLplateNum(maxhN);
end
end
end
%------HIDE 22222222222222222-----
if get(ghandles.rotPB2,'value')==1 && OLay==2, %
% Hide
if get(ghandles.rotPB2,'value')==1 && OLay==2, %
for j=1:length(Exp(OLay).hOL(:)) %Set all traces blue
try set(Exp(OLay).hOL(i),'color',[0 0 1]), catch, end
end
@@ -464,7 +425,7 @@ if get(ghandles.rotPB2,'value')==1 && OLay==2, %
set(Exp(OLay).hOL(i),'Visible','off')
set(Exp(OLay).hOLb(i),'Visible','off')
for j=1:length(Exp(OLay).hOL(:))
try if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN= j; end, catch end
try if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN=j; end, catch end
end
end
if htargetAxes==Exp(OLay).hOL(i), break;end
@@ -474,28 +435,27 @@ if get(ghandles.rotPB2,'value')==1 && OLay==2, %
if OLay==2
try if length(char(Exp(OLay).hOLname(maxhN)))>40,set(ghandles.OLay2,'FontSize',8);end, catch, end
set(ghandles.OLay2,'string', Exp(OLay).hOLname(maxhN));
traceLab= char(Exp(OLay).hOLname(maxhN));
traceLab=char(Exp(OLay).hOLname(maxhN));
try if length(char(Exp(OLay).hOLexpNm(maxhN)))>40,set(ghandles.OLexp2,'FontSize',8);end, catch, end
set(ghandles.OLexp2,'string',Exp(OLay).hOLexpNm(maxhN));
OLresDir= Exp(OLay).hOLresDir(maxhN);
OLplateNum= Exp(OLay).hOLplateNum(maxhN);
OLresDir=Exp(OLay).hOLresDir(maxhN);
OLplateNum=Exp(OLay).hOLplateNum(maxhN);
end
end
end %if rotPB2 ....==1
%------HIDE 33333333333333-----
if get(ghandles.rotPB3,'value') ==1 && OLay==3,
%make all traces blue
% Hide 3
if get(ghandles.rotPB3,'value') ==1 && OLay==3,
% make all traces blue
for i=1:length(Exp(OLay).hOL(:))
try set(Exp(OLay).hOL(i),'color',[0 0 1]), catch, end
end
for i=1:length(Exp(OLay).hOL(:))
if htargetAxes==Exp(OLay).hOL(i)
hidAx3traceN=i
set(Exp(OLay).hOL(i),'Visible','off')
set(Exp(OLay).hOLb(i),'Visible','off')
for j=1:length(Exp(OLay).hOL(:))
try if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN= j; end, catch, end
try if isequal(get(Exp(OLay).hOL(j),'Visible'),'on'), maxhN=j; end, catch, end
end
end
if htargetAxes==Exp(OLay).hOL(i), break;end
@@ -505,145 +465,129 @@ if get(ghandles.rotPB3,'value') ==1 && OLay==3,
if OLay==3
try if length(char(Exp(OLay).hOLname(maxhN)))>40,set(ghandles.OLay3,'FontSize',8);end, catch, end
set(ghandles.OLay3,'string', Exp(OLay).hOLname(maxhN));
traceLab= char(Exp(OLay).hOLname(maxhN));
traceLab=char(Exp(OLay).hOLname(maxhN));
try if length(char(Exp(OLay).hOLexpNm(maxhN)))>40,set(ghandles.OLexp3,'FontSize',8);end, catch, end
set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(maxhN));
OLresDir= Exp(OLay).hOLresDir(maxhN);
OLplateNum= Exp(OLay).hOLplateNum(maxhN);
OLresDir=Exp(OLay).hOLresDir(maxhN);
OLplateNum=Exp(OLay).hOLplateNum(maxhN);
end
end
destcompMsg= 'Olay';
end
destcompMsg='Olay';
catch
msg='Not in OLay frame-axis 1'
msg='Not in OLay frame-axis 1'
end
%**********************************************************************************
NoOLay=0;
try
OLay
expN=OLay
EZdatatip= 2
EZdatatip=2
catch
NoOLay=1;
EZdatatip=1;
end
if get(ghandles.spotTog,'value')==1 && NoOLay
OLresDir= Exp(expN).Dexp(DexpN).resDir;
OLresDir=Exp(expN).Dexp(DexpN).resDir;
OLplateNum=plateNum;
imLoc= [picLoc1(2), picLoc1(1)];
imLoc=[picLoc1(2), picLoc1(1)];
EZspotview(expN,DexpN, imLoc,OLresDir,OLplateNum,NoOLay)
end
%*****GraphicPertibationComparison**15_821*OR Chrono Day Comparison******************
if strcmpi(Exp(expN).DexpType,'single')||...
strcmpi(Exp(expN).DexpType,'multi')
%************
EZdestComp %*
%************
elseif strcmpi(Exp(expN).DexpType,'chrono') && ...
length(Exp(expN).Dexp)>1
%*************
EZmDayTrend %**
%*************
% GraphicPertibationComparison**15_821*OR Chrono Day Comparison
if strcmpi(Exp(expN).DexpType,'single') ...
|| strcmpi(Exp(expN).DexpType,'multi')
EZdestComp
elseif strcmpi(Exp(expN).DexpType,'chrono') ...
&& length(Exp(expN).Dexp)>1
EZmDayTrend
end
%********************************
% spotTog && ~Hide && Olay Capture spot location for spotview May need to
% add DexpN BUT the OLresDir likely get spotview to where it needs to go.
try
if exist('OLay') %User clicked on an Overlay
if get(ghandles.spotTog,'value')==1 && get(ghandles.rotPB1,'value') ~=1 && OLay<4
msg='OLay with SpotTog On and Hide off'
pos_=strfind(traceLab,'_')
rcStr=traceLab(pos_(2)+1:pos_(3)-1)
cPos=findstr(rcStr,'c');
rUsr=str2num(rcStr(2:cPos-1));
cUsr=str2num(rcStr(cPos+1:end));
imLoc= [cUsr, (17-rUsr)]; %picLoc1 %transform horz user data to vert image for picLocation data
OLresDir %=Exp(expN).hOLresDir(traceN);
OLplateNum %=Exp(expN).hOLplateNum(traceN);
%********************************************************
EZspotview(expN, imLoc,OLresDir,OLplateNum,NoOLay) %*
%********************************************************
end
end
if exist('OLay') %User clicked on an Overlay
if get(ghandles.spotTog,'value')==1 && get(ghandles.rotPB1,'value') ~=1 && OLay<4
msg='OLay with SpotTog On and Hide off'
pos_=strfind(traceLab,'_')
rcStr=traceLab(pos_(2)+1:pos_(3)-1)
cPos=findstr(rcStr,'c');
rUsr=str2num(rcStr(2:cPos-1));
cUsr=str2num(rcStr(cPos+1:end));
imLoc=[cUsr, (17-rUsr)]; %picLoc1 %transform horz user data to vert image for picLocation data
OLresDir %=Exp(expN).hOLresDir(traceN);
OLplateNum %=Exp(expN).hOLplateNum(traceN);
EZspotview(expN, imLoc,OLresDir,OLplateNum,NoOLay)
end
end
catch
end
[output_txt]=datatipp(obj,event_obj);
%*********************HeatMap Text Field*********************************
% HeatMap Text Field
try
ll=num2str(l);
if length(ll)>5,htl= ll(1:5);else htl=ll;end
ll=num2str(l);
if length(ll)>5,htl=ll(1:5);else htl=ll;end
catch
htl=' ';
end
try
kk=num2str(K);
if length(kk)>5,htk= kk(1:5);else htk=kk;end
kk=num2str(K);
if length(kk)>5,htk=kk(1:5);else htk=kk;end
catch
htk=' ';
end
try
rr=num2str(r);
if length(rr)>5,htr= rr(1:5);else htr=rr;end
rr=num2str(r);
if length(rr)>5,htr=rr(1:5);else htr=rr;end
catch
htr=' ';
end
try
n1= num2str(Exp(expN).HtMpIntN1(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1= n1(1:5);else N1=n1; end
n1=num2str(Exp(expN).HtMpIntN1(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN1(indx));
if length(n1)>5,N1=n1(1:5);else N1=n1; end
htN1=strcat('_N1=',N1);
catch
htN1=' ';
end
try
n2= num2str(Exp(expN).HtMpIntN2(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN2(indx));
if length(n2)>5,N2= n2(1:5);else N2=n2; end
n2=num2str(Exp(expN).HtMpIntN2(indx)); %num2str(Exp(expN).Dexp(DexpN).HtMpIntN2(indx));
if length(n2)>5,N2=n2(1:5);else N2=n2; end
htN2=strcat('_N2=',N2);
catch
htN2=' ';
end
if Exp(expN).htmapPBsel==1, htmapStr= strcat('K= ',htk); end
if Exp(expN).htmapPBsel==2, htmapStr= strcat('r= ',htr); end
if Exp(expN).htmapPBsel==1, htmapStr=strcat('K=',htk); end
if Exp(expN).htmapPBsel==2, htmapStr=strcat('r=',htr); end
try
if Exp(expN).htmapPBsel==0 || Exp(expN).htmapPBsel>2
htmapStr=strcat('L= ',htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
if Exp(expN).htmapPBsel==0 || Exp(expN).htmapPBsel>2
htmapStr=strcat('L=',htl, htN1,htN2)
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
try
if Exp(expN).htmapPBsel==1 || Exp(expN).htmapPBsel==2
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
if Exp(expN).htmapPBsel==1 || Exp(expN).htmapPBsel==2
if expN==1,set(ghandles.HtMapVals1,'string',htmapStr);end
if expN==2,set(ghandles.HtMapVals2,'string',htmapStr);end
if expN==3,set(ghandles.HtMapVals3,'string',htmapStr);end
end
catch
end
%datacursormode(gcf)
%**********************************************Test Area
%Added 18_0105 to define RFcmpGFlg for EZmDayTrend.m when an Image spot
%is clicked
% datacursormode(gcf)
% Test Area
% Added 18_0105 to define RFcmpGFlg for EZmDayTrend.m when an Image spot
% is clicked
tempLB= str2mat(selGnOrf)
tempLB=str2mat(selGnOrf)
RFcmpGFlg=0;
if isequal(tempLB(4:6),'cmp'), RFnum= str2double(tempLB(3));
if isequal(tempLB(4:6),'cmp'), RFnum=str2double(tempLB(3));
elseif isequal(tempLB(3:6),'cmpG'), RFcmpGFlg=1;
elseif isequal(tempLB(3:6),'cmpP'), RFcmpGFlg=1; %I beleive handling will be the same as RFcmpG
end

125
workflow/apps/matlab/ezview/EZvFigPrint.m
View File

@@ -1,25 +1,23 @@
%EZvFigPrint.m Called by [P} button to produce S curves for publication
% EZvFigPrint.m Called by [P} button to produce S curves for publication
global ghandles
global Exp
try
lnwidth= str2num(Exp(4).plotPars{1})
axisFontSz= str2num(Exp(4).plotPars{2})
legFontSz= str2num(Exp(4).plotPars{3})
markerSz= str2num(Exp(4).plotPars{4})
lnwidth=str2num(Exp(4).plotPars{1})
axisFontSz=str2num(Exp(4).plotPars{2})
legFontSz=str2num(Exp(4).plotPars{3})
markerSz=str2num(Exp(4).plotPars{4})
catch
lnwidth=4;
axisFontSz=36;
legFontSz= 10;
legFontSz=10;
markerSz=5;
end
if get(ghandles.printOL1,'Value')==1,zone= 1; end
if get(ghandles.printOL2,'Value')==1,zone= 2; end
if get(ghandles.printOL3,'Value')==1,zone= 3; end
if get(ghandles.printOL1,'Value')==1,zone=1; end
if get(ghandles.printOL2,'Value')==1,zone=2; end
if get(ghandles.printOL3,'Value')==1,zone=3; end
semiLog=0;
if isequal(get(ghandles.OLaxes1,'YScale'),'log'), semiLog=1;end
@@ -29,26 +27,25 @@ clear legName tmp
figure
set(gcf,'OuterPosition',(get(0,'screensize')))
hn=0;
if isequal(get(Exp(zone).hOL(1),'Visible'),'on')
disphOLX(1)= {get(Exp(zone).hOL(1),'XData')}
disphOLY(1)= {get(Exp(zone).hOL(1),'YData')}
hn=0;
if isequal(get(Exp(zone).hOL(1),'Visible'),'on')
disphOLX(1)={get(Exp(zone).hOL(1),'XData')}
disphOLY(1)={get(Exp(zone).hOL(1),'YData')}
tmp(1)=strrep(Exp(zone).hOLname(1),'_','-')
try
disphOLbX(1)= {get(Exp(zone).hOLb(1),'XData')}
disphOLbY(1)= {get(Exp(zone).hOLb(1),'YData')}
catch end
try
disphOLbX(1)={get(Exp(zone).hOLb(1),'XData')}
disphOLbY(1)={get(Exp(zone).hOLb(1),'YData')}
catch end
hn=hn+1
notDup=1;
end
end
notDup=0;
for hN=2:length(Exp(zone).hOL)
%Bounce-dupicate data removal
% Bounce-dupicate data removal
for j=1:(hN-1)
if isequal(Exp(zone).hOLname(hN), Exp(zone).hOLname(j))%&& ...
%isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
% isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
notDup=0;
break
else
@@ -59,46 +56,43 @@ for hN=2:length(Exp(zone).hOL)
if isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
hn=hn+1
try
disphOLX(hn)= {get(Exp(zone).hOL(hN),'XData')};
disphOLY(hn)= {get(Exp(zone).hOL(hN),'YData')};
disphOLX(hn)={get(Exp(zone).hOL(hN),'XData')};
disphOLY(hn)={get(Exp(zone).hOL(hN),'YData')};
tmp(hn)=strrep(Exp(zone).hOLname(hN),'_','-')
try
disphOLbX(hn)={get(Exp(zone).hOLb(hN),'XData')};
disphOLbY(hn)= {get(Exp(zone).hOLb(hN),'YData')};
catch end
disphOLbY(hn)={get(Exp(zone).hOLb(hN),'YData')};
catch
end
tmp(hn)=strrep(Exp(zone).hOLname(hN),'_','-')
catch ME
disp(ME)
display('error leading to line 59 catch')
end
end
end
end
end
end
end
end
for i=1:hn
for i=1:hn
if semiLog==0
hprint=plot(cell2mat(disphOLX(i)),cell2mat(disphOLY(i)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 6
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(i)={get(hprint,'color')};
else
hprint=semilogy(cell2mat(disphOLX(i)),cell2mat(disphOLY(i)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 4.0
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(i)={get(hprint,'color')};
end
hold all
end
hold all
end
if Exp(zone).CompositPlot~=1 %Standard plot, Not a Composite Plot
legName= tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
try
if Exp(zone).CompositPlot~=1 % Standard plot, Not a Composite Plot
legName=tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
try
for i=1:hn
if semiLog==0
hprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
@@ -106,43 +100,35 @@ try
hprint=semilogy(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
end
end
catch end
hold off
%*******End of Standard Overlay Plot***********************
else %if Composite Plot
catch
end
hold off
% End of Standard Overlay Plot
else % if Composite Plot
for hcN=1:(Exp(zone).cTraceN -1)
disphOLX(hcN)= {get(Exp(zone).hCmean(hcN),'XData')};
disphOLY(hcN)= {get(Exp(zone).hCmean(hcN),'YData')};
disphOLX(hcN)={get(Exp(zone).hCmean(hcN),'XData')};
disphOLY(hcN)={get(Exp(zone).hCmean(hcN),'YData')};
disphOLbX(hcN)={get(Exp(zone).hBound1(hcN),'XData')};
disphOLbY(hcN)= {get(Exp(zone).hBound1(hcN),'YData')};
disphOLbY(hcN)={get(Exp(zone).hBound1(hcN),'YData')};
disphOLcX(hcN)={get(Exp(zone).hBound2(hcN),'XData')};
disphOLcY(hcN)= {get(Exp(zone).hBound2(hcN),'YData')};
disphOLcY(hcN)={get(Exp(zone).hBound2(hcN),'YData')};
tmp(hcN)=(Exp(zone).cName(hcN))
if semiLog==0
hprint=plot(cell2mat(disphOLX(hcN)),cell2mat(disphOLY(hcN)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 6
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(hcN)={get(hprint,'color')};
else
hprint=semilogy(cell2mat(disphOLX(hcN)),cell2mat(disphOLY(hcN)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 4.0
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(hcN)={get(hprint,'color')};
end
hold all
legName= tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
%{
hold all
legName=tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
%{
for i=1:hn
hprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
end
@@ -150,15 +136,12 @@ set(hleg,'fontsize',legFontSz)
end
for i=1:(Exp(zone).cTraceN -1)
hBprint= plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)))
hBprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)))
set(hBprint,'linewidth',.5) %lnwidth) %0.5 then 1.5 now 6
set(hBprint,'color',linecolor{i})
hCprint= plot(cell2mat(disphOLcX(i)),cell2mat(disphOLcY(i)))
hCprint=plot(cell2mat(disphOLcX(i)),cell2mat(disphOLcY(i)))
set(hCprint,'linewidth',0.5) %lnwidth) %0.5 then 1.5 now 6
set(hBprint,'color',linecolor{i})
end
hold off
end
end

10
workflow/apps/matlab/ezview/EZvImagesOnly.m
View File

@@ -1,15 +1,13 @@
%EZvImagesOnly
% EZvImagesOnly
asd=12
dirLst=dir(ExpPath)
for i=1:size(dirLst,1)
if ~isempty(str2num(dirLst(i).name)) || ~isempty(strfind(dirLst(i).name,'Scan')) % && jpgOut==1
scLst= fullfile(ExpPath,dirLst(i).name);
scLst=fullfile(ExpPath,dirLst(i).name);
for n=1:size(filelst,1)
try
if ~isempty(strfind(filelst(n).name,'bmp'))||~isempty(strfind(filelst(n).name,'tif'))
tptImLst(n)=filelst(n).name;
end
catch
end
@@ -18,7 +16,8 @@ for i=1:size(dirLst,1)
end
scLength=length(scLst);
end
I= imread(ExpOutImFile);
I=imread(ExpOutImFile);
expAxes=handles.Iaxes1;
imshow(I)
set(expAxes,'xtick',[],'ytick',[])
@@ -29,4 +28,3 @@ expAxes=handles.Iaxes3;
imshow(I)
set(expAxes,'xtick',[],'ytick',[])

1026
workflow/apps/matlab/ezview/EZvInitLoad.m
View File

File diff suppressed because it is too large Load Diff

54
workflow/apps/matlab/ezview/EZvNIcircle.m
View File

@@ -1,11 +1,11 @@
%Disk Image
% Disk Image
%{
%Imaging ToolBox method
r=14;
A=zeros(70,70); %(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt)))
m= {40,40};
m={40,40};
A(m{:})=1;
B= imdilate(A,strel('disk',r,0) );
B=imdilate(A,strel('disk',r,0) );
imshow(B)
area=pi*r^2
@@ -18,45 +18,39 @@ clear all
%A=zeros(70,70);
%A=zeros(r,r);
%P=[40,40];
%center= [refPtR+ round(.5*width), refPtC+ round(.5*width)];
%center=[refPtR+ round(.5*width), refPtC+ round(.5*width)];
%A=zeros(70,70);
%---------------------------------------------------------------------
%radius=14;
diaExt=2*(radius+1);
circBoxA=zeros(diaExt,diaExt);
center= [radius+2, radius+2];
center=[radius+2, radius+2];
[m n ]=size(circBoxA);
X=bsxfun(@plus,(1:m)', zeros(1,n));
Y=bsxfun(@plus,(1:n), zeros(m,1));
cirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radius;
cirMask=sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radius;
area=pi*radius^2;
cirPixA=nnz(cirMask);
optCirMask=double(cirMask);
optCirMask(optCirMask==0)=0.8;
cirPixA= nnz(cirMask);
optCirMask= double(cirMask);
optCirMask(optCirMask==0)= 0.8;
%+++++++++++Foto Circle Fram(e)+++++++++++++++++++++
% Foto Circle Fram(e)
expansion=2;
radExpan= radius+expansion;
radExpan=radius+expansion;
FdiaExt=2*(radExpan);
circBoxA=zeros(FdiaExt,FdiaExt);
center= [radExpan+1, radExpan+1];
center=[radExpan+1, radExpan+1];
[m n ]=size(circBoxA);
X=bsxfun(@plus,(1:m)', zeros(1,n));
Y=bsxfun(@plus,(1:n), zeros(m,1));
FcirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radExpan;
%FcirPixA= nnz(cirMask);
FoptCirMask= double(FcirMask);
FoptCirMask(FoptCirMask==1)= 2;
%FoptCirMask(FoptCirMask==0)= 1;
%********Combine Masks to create circular boundry************
padOptCirMask= padarray(optCirMask,[expansion-1 expansion-1],0.8);
FoptCirMask= FoptCirMask .* padOptCirMask;
FoptCirMask(FoptCirMask==1.6)= 0.8;
FoptCirMask(FoptCirMask==0)= 1;
FoptCirMask(FoptCirMask==2)= 1;
%---------------------------------------------------
%imagesc(cirMask)
FcirMask=sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radExpan;
% FcirPixA=nnz(cirMask);
FoptCirMask=double(FcirMask);
FoptCirMask(FoptCirMask==1)=2;
% FoptCirMask(FoptCirMask==0)=1;
% Combine Masks to create circular boundry
padOptCirMask=padarray(optCirMask,[expansion-1 expansion-1],0.8);
FoptCirMask=FoptCirMask .* padOptCirMask;
FoptCirMask(FoptCirMask==1.6)=0.8;
FoptCirMask(FoptCirMask==0)=1;
FoptCirMask(FoptCirMask==2)=1;
% imagesc(cirMask)

108
workflow/apps/matlab/ezview/EZvTrendPrint.m
View File

@@ -3,48 +3,45 @@
global ghandles
global Exp
try
lnwidth= str2num(Exp(4).plotPars{1})
axisFontSz= str2num(Exp(4).plotPars{2})
legFontSz= str2num(Exp(4).plotPars{3})
markerSz= str2num(Exp(4).plotPars{4})
lnwidth=str2num(Exp(4).plotPars{1})
axisFontSz=str2num(Exp(4).plotPars{2})
legFontSz=str2num(Exp(4).plotPars{3})
markerSz=str2num(Exp(4).plotPars{4})
catch
lnwidth=4;
axisFontSz=36;
legFontSz= 10;
legFontSz=10;
markerSz=5;
end
if get(ghandles.printOL1,'Value')==1,zone= 1; end
if get(ghandles.printOL2,'Value')==1,zone= 2; end
if get(ghandles.printOL3,'Value')==1,zone= 3; end
if get(ghandles.printOL1,'Value')==1,zone=1; end
if get(ghandles.printOL2,'Value')==1,zone=2; end
if get(ghandles.printOL3,'Value')==1,zone=3; end
clear legName tmp
figure
set(gcf,'OuterPosition',(get(0,'screensize')))
hn=0;
if isequal(get(Exp(zone).hOL(1),'Visible'),'on')
disphOLX(1)= {get(Exp(zone).hOL(1),'XData')}
disphOLY(1)= {get(Exp(zone).hOL(1),'YData')}
hn=0;
if isequal(get(Exp(zone).hOL(1),'Visible'),'on')
disphOLX(1)={get(Exp(zone).hOL(1),'XData')}
disphOLY(1)={get(Exp(zone).hOL(1),'YData')}
tmp(1)=strrep(Exp(zone).hOLname(1),'_','-')
try
disphOLbX(1)= {get(Exp(zone).hOLb(1),'XData')}
disphOLbY(1)= {get(Exp(zone).hOLb(1),'YData')}
disphOLbX(1)={get(Exp(zone).hOLb(1),'XData')}
disphOLbY(1)={get(Exp(zone).hOLb(1),'YData')}
catch end
hn=hn+1
notDup=1;
end
notDup=0;
notDup=0;
for hN=2:length(Exp(zone).hOL)
%Bounce-dupicate data removal
for hN=2:length(Exp(zone).hOL)
% Bounce-dupicate data removal
for j=1:(hN-1)
if isequal(Exp(zone).hOLname(hN), Exp(zone).hOLname(j))%&& ...
%isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
if isequal(Exp(zone).hOLname(hN), Exp(zone).hOLname(j)) %&& ...
% isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
notDup=0;
break
else
@@ -55,18 +52,18 @@ for hN=2:length(Exp(zone).hOL)
if isequal(get(Exp(zone).hOL(hN),'Visible'),'on')
hn=hn+1
try
disphOLX(hn)= {get(Exp(zone).hOL(hN),'XData')};
disphOLY(hn)= {get(Exp(zone).hOL(hN),'YData')};
disphOLX(hn)={get(Exp(zone).hOL(hN),'XData')};
disphOLY(hn)={get(Exp(zone).hOL(hN),'YData')};
tmp(hn)=strrep(Exp(zone).hOLname(hN),'_','-')
try
disphOLbX(hn)={get(Exp(zone).hOLb(hN),'XData')};
disphOLbY(hn)= {get(Exp(zone).hOLb(hN),'YData')};
catch end
disphOLbY(hn)={get(Exp(zone).hOLb(hN),'YData')};
catch
end
tmp(hn)=strrep(Exp(zone).hOLname(hN),'_','-')
catch ME
disp(ME)
display('error leading to line 59 catch')
end
end
end
@@ -78,23 +75,20 @@ for hN=2:length(Exp(zone).hOL)
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 6
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(i)={get(hprint,'color')};
else
hprint=semilogy(cell2mat(disphOLX(i)),cell2mat(disphOLY(i)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 4.0
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(i)={get(hprint,'color')};
end
hold all
hold all
end
if Exp(zone).CompositPlot~=1 %Standard plot, Not a Composite Plot
legName= tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
try
if Exp(zone).CompositPlot~=1 % Standard plot, Not a Composite Plot
legName=tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
try
for i=1:hn
if semiLog==0
hprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
@@ -102,19 +96,19 @@ try
hprint=semilogy(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
end
end
catch end
catch
end
hold off
%*******End of Standard Overlay Plot***********************
else %if Composite Plot
hold off
% End of Standard Overlay Plot
else %if Composite Plot
for hcN=1:(Exp(zone).cTraceN -1)
disphOLX(hcN)= {get(Exp(zone).hCmean(hcN),'XData')};
disphOLY(hcN)= {get(Exp(zone).hCmean(hcN),'YData')};
disphOLX(hcN)={get(Exp(zone).hCmean(hcN),'XData')};
disphOLY(hcN)={get(Exp(zone).hCmean(hcN),'YData')};
disphOLbX(hcN)={get(Exp(zone).hBound1(hcN),'XData')};
disphOLbY(hcN)= {get(Exp(zone).hBound1(hcN),'YData')};
disphOLbY(hcN)={get(Exp(zone).hBound1(hcN),'YData')};
disphOLcX(hcN)={get(Exp(zone).hBound2(hcN),'XData')};
disphOLcY(hcN)= {get(Exp(zone).hBound2(hcN),'YData')};
disphOLcY(hcN)={get(Exp(zone).hBound2(hcN),'YData')};
tmp(hcN)=(Exp(zone).cName(hcN))
if semiLog==0
@@ -122,7 +116,6 @@ hold off
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 6
set(gca,'fontsize',axisFontSz) % 8 to 15 to 21
linecolor(hcN)={get(hprint,'color')};
else
hprint=semilogy(cell2mat(disphOLX(hcN)),cell2mat(disphOLY(hcN)))
set(hprint,'linewidth',lnwidth) %0.5 then 1.5 now 4.0
@@ -130,31 +123,24 @@ hold off
linecolor(hcN)={get(hprint,'color')};
end
hold all
legName= tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
%{
hold all
legName=tmp
hleg=legend((legName),'location','NEO')
set(hleg,'fontsize',legFontSz)
%{
for i=1:hn
hprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)),'marker','+','markerEdgeColor',cell2mat(linecolor(i)),'markerSize',markerSz, 'linestyle','none')
end
%}
end
for i=1:(Exp(zone).cTraceN -1)
hBprint= plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)))
hBprint=plot(cell2mat(disphOLbX(i)),cell2mat(disphOLbY(i)))
set(hBprint,'linewidth',.5) %lnwidth) %0.5 then 1.5 now 6
set(hBprint,'color',linecolor{i})
hCprint= plot(cell2mat(disphOLcX(i)),cell2mat(disphOLcY(i)))
hCprint=plot(cell2mat(disphOLcX(i)),cell2mat(disphOLcY(i)))
set(hCprint,'linewidth',0.5) %lnwidth) %0.5 then 1.5 now 6
set(hBprint,'color',linecolor{i})
end
hold off
end
end

2
workflow/apps/matlab/ezview/EZvapendLabel.m
View File

@@ -1,4 +1,4 @@
% Create the text in an axis:
% Create the text in an axis
hFstrip=figure;
%figure(hFstrip,'Visible','off')

254
workflow/apps/matlab/ezview/EZviewGui.m
View File

@@ -155,10 +155,10 @@ function [output_txt]=myupdatefcn(obj,event_obj)
global Exp
[output_txt]=datatipp(obj,event_obj); % datatipp is a Matlab function
gcf= Exp(4).guiFig; % gcf= ghandles.figure1 Mathworks Provided this line for Apple issue
gcf=Exp(4).guiFig; % gcf=ghandles.figure1 Mathworks Provided this line for Apple issue
clkPos=getCursorInfo(datacursormode(gcf));
cpos=clkPos.Position;
htargetAxes= clkPos.Target;
htargetAxes=clkPos.Target;
% datacursormode(gcf)
if ghandles.Iaxes1==get(htargetAxes,'Parent')||...
ghandles.Iaxes2==get(htargetAxes,'Parent')||...
@@ -212,12 +212,12 @@ function MPed1_Callback(hObject, eventdata, handles)
input=get(hObject,'String');
Max=floor(get(handles.MPsldr1,'max'));
Min=floor(get(handles.MPsldr1,'min'));
if str2num(input) >= Min && str2num(input) <= Max
if str2num(input) >=Min && str2num(input) <=Max
display(input)
set(handles.MPsldr1,'value',str2double(input));
else
if str2double(input) >= Max, set(handles.MPsldr1,'value',Max); set(handles.MPed1,'string',num2str(Max));end
if str2double(input) <= Min, set(handles.MPsldr1,'value',Min),set(handles.MPed1,'string',num2str(Min));end
if str2double(input) >=Max, set(handles.MPsldr1,'value',Max); set(handles.MPed1,'string',num2str(Max));end
if str2double(input) <=Min, set(handles.MPsldr1,'value',Min),set(handles.MPed1,'string',num2str(Min));end
end
EZVimDisplay
@@ -232,7 +232,7 @@ function MPed1_Callback(hObject, eventdata, handles)
function MPed1_CreateFcn(hObject, eventdata, handles)
global ghandles
global Exp
ghandles.guiFig= gcf;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
@@ -271,12 +271,12 @@ function DMed1_Callback(hObject, eventdata, handles)
Max=floor(get(handles.DMsldr1,'max'));
Min=floor(get(handles.DMsldr1,'min'));
input=get(hObject,'String')
if str2num(input) >= Min && str2num(input) <= Max
if str2num(input) >=Min && str2num(input) <=Max
display(input)
set(handles.DMsldr1,'value',str2double(input))
else
if str2num(input) >= Max, set(handles.DMsldr1,'value',Max); set(handles.DMed1,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.DMsldr1,'value',Min),set(handles.DMed1,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.DMsldr1,'value',Max); set(handles.DMed1,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.DMsldr1,'value',Min),set(handles.DMed1,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -298,7 +298,7 @@ function Tptsldr1_Callback(hObject, eventdata, handles)
input=floor(get(hObject,'value'));
display(input)
set(handles.Tpted1,'string',num2str(floor(input)))
prntHt= 0;
prntHt=0;
EZVimDisplay
% Executes during object creation, after setting all properties.
@@ -319,12 +319,12 @@ function Tpted1_Callback(hObject, eventdata, handles)
input=get(hObject,'String')
Max=floor(get(handles.Tptsldr1,'max'));
Min=floor(get(handles.Tptsldr1,'min'));
if str2double(input) >= Min && str2double(input) <= Max
if str2double(input) >=Min && str2double(input) <=Max
display(input)
set(handles.Tptsldr1,'value',str2double(input))
else
if str2num(input) >= Max, set(handles.Tptsldr1,'value',Max); set(handles.Tpted1,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.Tptsldr1,'value',Min),set(handles.Tpted1,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.Tptsldr1,'value',Max); set(handles.Tpted1,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.Tptsldr1,'value',Min),set(handles.Tpted1,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -365,12 +365,12 @@ function clrOlay1_Callback(hObject, eventdata, handles)
set(ghandles.OLay1,'string',{' '})
set(ghandles.OLexp1,'string',{''})
cla(ghandles.OLaxes1)
Exp(1).traceN= 0;
%Exp(1).cTraceN= 0;
Exp(1).hOL =[]; Exp(1).hOLb=[];
Exp(1).traceN=0;
%Exp(1).cTraceN=0;
Exp(1).hOL=[]; Exp(1).hOLb=[];
Exp(1).hOLname={}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={};
Exp(1).hOLplateNum=[];
Exp(1).hOLresDir= {};
Exp(1).hOLresDir={};
cla(ghandles.Dlaxes1); cla(ghandles.Dkaxes1); cla(ghandles.Draxes1);
cla(ghandles.DNLaxes1);
Exp(1).hL =[]; Exp(1).hLb=[];
@@ -383,15 +383,15 @@ function clrOlay1_Callback(hObject, eventdata, handles)
Exp(1).hintLadj =[]; Exp(1).hintLadjb=[]; % 2016_0222
% reset Composite Overlay plot to initialization values
Exp(1).cTraceN= 1;
Exp(1).ll= []; Exp(1).rr= []; Exp(1).kk= [];
Exp(1).cLmean= []; Exp(1).cRmean= []; Exp(1).cKmean= [];
Exp(1).cTraceIndx= 1;
Exp(1).cTraceN=1;
Exp(1).ll=[]; Exp(1).rr=[]; Exp(1).kk=[];
Exp(1).cLmean=[]; Exp(1).cRmean=[]; Exp(1).cKmean=[];
Exp(1).cTraceIndx=1;
Exp(1).hCmean=[];
Exp(1).hBound1= [];
Exp(1).hBound2= [];
Exp(1).hBound1=[];
Exp(1).hBound2=[];
Exp(1).CompositPlot=0;
Exp(1).Trace= []; %added for Trend BoxPlot data 17_1114
Exp(1).Trace=[]; %added for Trend BoxPlot data 17_1114
end
% Executes on slider movement.
@@ -427,15 +427,15 @@ function MPed2_Callback(hObject, eventdata, handles)
input=get(hObject,'String');
Max=floor(get(handles.MPsldr2,'max'));
Min=floor(get(handles.MPsldr2,'min'));
if str2num(input) >= Min && str2num(input) <= Max
if str2num(input) >=Min && str2num(input) <=Max
display(input)
set(handles.MPsldr2,'value',str2double(input));
else
if str2num(input) >= Max, set(handles.MPsldr2,'value',Max); set(handles.MPed2,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.MPsldr2,'value',Min),set(handles.MPed2,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.MPsldr2,'value',Max); set(handles.MPed2,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.MPsldr2,'value',Min),set(handles.MPed2,'string',num2str(Min));end
end
EZVimDisplay
ghandles.guiFig= gcf;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
@@ -449,7 +449,7 @@ function MPed2_CreateFcn(hObject, eventdata, handles)
% hObject handle to MPed2 (see GCBO)
global ghandles
global Exp
ghandles.guiFig= gcf;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
@@ -488,12 +488,12 @@ function DMed2_Callback(hObject, eventdata, handles)
Max=floor(get(handles.DMsldr2,'max'));
Min=floor(get(handles.DMsldr2,'min'));
input=get(hObject,'String')
if str2double(input) >= Min && str2double(input) <= Max
if str2double(input) >=Min && str2double(input) <=Max
display(input)
set(handles.DMsldr2,'value',str2double(input))
else
if str2double(input) >= Max, set(handles.DMsldr2,'value',Max); set(handles.DMed2,'string',num2str(Max));end
if str2double(input) <= Min, set(handles.DMsldr2,'value',Min),set(handles.DMed2,'string',num2str(Min));end
if str2double(input) >=Max, set(handles.DMsldr2,'value',Max); set(handles.DMed2,'string',num2str(Max));end
if str2double(input) <=Min, set(handles.DMsldr2,'value',Min),set(handles.DMed2,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -518,7 +518,7 @@ function Tptsldr2_Callback(hObject, eventdata, handles)
input=floor(get(hObject,'value'));
display(input)
set(handles.Tpted2,'string',num2str(floor(input)))
prntHt= 0;
prntHt=0;
EZVimDisplay
end
@@ -539,12 +539,12 @@ function Tpted2_Callback(hObject, eventdata, handles)
input=get(hObject,'String')
Max=floor(get(handles.Tptsldr2,'max'));
Min=floor(get(handles.Tptsldr2,'min'));
if str2double(input) >= Min && str2double(input) <= Max
if str2double(input) >=Min && str2double(input) <=Max
display(input)
set(handles.Tptsldr2,'value',str2double(input))
else
if str2num(input) >= Max, set(handles.Tptsldr2,'value',Max); set(handles.Tpted2,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.Tptsldr2,'value',Min),set(handles.Tpted2,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.Tptsldr2,'value',Max); set(handles.Tpted2,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.Tptsldr2,'value',Min),set(handles.Tpted2,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -562,7 +562,7 @@ function expSelPB2_Callback(hObject, eventdata, handles)
% hObject handle to expSelPB2 (see GCBO)
global Exp
expN=2;
prntHt= 0;
prntHt=0;
EZexpSel
end
@@ -583,13 +583,13 @@ function clrOlay2_Callback(hObject, eventdata, handles)
set(ghandles.OLay2,'string',{''})
set(ghandles.OLexp2,'string',{''})
cla(ghandles.OLaxes2)
Exp(2).traceN= 0;
%Exp(2).cTraceN= 0;
Exp(2).traceN=0;
%Exp(2).cTraceN=0;
Exp(2).hOL =[]; Exp(2).hOLb=[];
Exp(2).hOLname={}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
Exp(2).hOLplateNum=[];
Exp(2).hOLresDir= {};
Exp(2).hOLresDir={};
cla(ghandles.Dlaxes2); cla(ghandles.Dkaxes2); cla(ghandles.Draxes2);
cla(ghandles.DNLaxes2); % 2016_0222
@@ -601,15 +601,15 @@ function clrOlay2_Callback(hObject, eventdata, handles)
Exp(2).rRF1=[]; Exp(2).hrRF2=[];
%reset Composite Overlay plot to initialization values
Exp(2).cTraceN= 1;
Exp(2).ll= []; Exp(2).rr= []; Exp(2).kk= [];
Exp(2).cLmean= []; Exp(2).cRmean= []; Exp(2).cKmean= [];
Exp(2).cTraceIndx= 1;
Exp(2).cTraceN=1;
Exp(2).ll=[]; Exp(2).rr=[]; Exp(2).kk=[];
Exp(2).cLmean=[]; Exp(2).cRmean=[]; Exp(2).cKmean=[];
Exp(2).cTraceIndx=1;
Exp(2).hCmean=[];
Exp(2).hBound1= [];
Exp(2).hBound2= [];
Exp(2).hBound1=[];
Exp(2).hBound2=[];
Exp(2).CompositPlot=0;
Exp(2).Trace= []; %added for Trend BoxPlot data 17_1114
Exp(2).Trace=[]; %added for Trend BoxPlot data 17_1114
end
@@ -646,15 +646,15 @@ function MPed3_Callback(hObject, eventdata, handles)
input=get(hObject,'String');
Max=floor(get(handles.MPsldr3,'max'));
Min=floor(get(handles.MPsldr3,'min'));
if str2num(input) >= Min && str2num(input) <= Max
if str2num(input) >=Min && str2num(input) <=Max
display(input)
set(handles.MPsldr3,'value',str2double(input));
else
if str2num(input) >= Max, set(handles.MPsldr3,'value',Max); set(handles.MPed3,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.MPsldr3,'value',Min),set(handles.MPed3,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.MPsldr3,'value',Max); set(handles.MPed3,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.MPsldr3,'value',Min),set(handles.MPed3,'string',num2str(Min));end
end
EZVimDisplay
ghandles.guiFig= gcf;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
@@ -666,7 +666,7 @@ end
function MPed3_CreateFcn(hObject, eventdata, handles)
global ghandles
global Exp
ghandles.guiFig= gcf;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
@@ -704,12 +704,12 @@ function DMed3_Callback(hObject, eventdata, handles)
Max=floor(get(handles.DMsldr3,'max'));
Min=floor(get(handles.DMsldr3,'min'));
input=get(hObject,'String')
if str2num(input) >= Min && str2num(input) <= Max
if str2num(input) >=Min && str2num(input) <=Max
display(input)
set(handles.DMsldr3,'value',str2double(input))
else
if str2num(input) >= Max, set(handles.DMsldr3,'value',Max); set(handles.DMed3,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.DMsldr3,'value',Min),set(handles.DMed3,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.DMsldr3,'value',Max); set(handles.DMed3,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.DMsldr3,'value',Min),set(handles.DMed3,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -732,7 +732,7 @@ function Tptsldr3_Callback(hObject, eventdata, handles)
input=floor(get(hObject,'value'));
display(input)
set(handles.Tpted3,'string',num2str(floor(input)))
prntHt= 0;
prntHt=0;
EZVimDisplay
end
@@ -753,12 +753,12 @@ function Tpted3_Callback(hObject, eventdata, handles)
input=get(hObject,'String')
Max=floor(get(handles.Tptsldr3,'max'));
Min=floor(get(handles.Tptsldr3,'min'));
if str2double(input) >= Min && str2double(input) <= Max
if str2double(input) >=Min && str2double(input) <=Max
display(input)
set(handles.Tptsldr3,'value',str2double(input))
else
if str2num(input) >= Max, set(handles.Tptsldr3,'value',Max); set(handles.Tpted3,'string',num2str(Max));end
if str2num(input) <= Min, set(handles.Tptsldr3,'value',Min),set(handles.Tpted3,'string',num2str(Min));end
if str2num(input) >=Max, set(handles.Tptsldr3,'value',Max); set(handles.Tpted3,'string',num2str(Max));end
if str2num(input) <=Min, set(handles.Tptsldr3,'value',Min),set(handles.Tpted3,'string',num2str(Min));end
end
EZVimDisplay
end
@@ -797,13 +797,13 @@ function clrOlay3_Callback(hObject, eventdata, handles)
set(ghandles.OLay3,'string',{''})
set(ghandles.OLexp3,'string',{''})
cla(ghandles.OLaxes3);
Exp(3).traceN= 0;
%Exp(3).cTraceN= 0;
Exp(3).traceN=0;
%Exp(3).cTraceN=0;
Exp(3).hOL =[]; Exp(3).hOLb=[];
Exp(3).hOLname={}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
Exp(3).hOLplateNum=[];
Exp(3).hOLresDir= {};
Exp(3).hOLresDir={};
cla(ghandles.Dlaxes3); cla(ghandles.Dkaxes3); cla(ghandles.Draxes3);
cla(ghandles.DNLaxes3);% 2016_0222
@@ -815,15 +815,15 @@ function clrOlay3_Callback(hObject, eventdata, handles)
Exp(3).rRF1=[]; Exp(3).hrRF2=[];
% Reset Composite Overlay plot to initialization values
Exp(3).cTraceN= 1;
Exp(3).ll= []; Exp(3).rr= []; Exp(3).kk= [];
Exp(3).cLmean= []; Exp(3).cRmean= []; Exp(3).cKmean= [];
Exp(3).cTraceIndx= 1;
Exp(3).cTraceN=1;
Exp(3).ll=[]; Exp(3).rr=[]; Exp(3).kk=[];
Exp(3).cLmean=[]; Exp(3).cRmean=[]; Exp(3).cKmean=[];
Exp(3).cTraceIndx=1;
Exp(3).hCmean=[];
Exp(3).hBound1= [];
Exp(3).hBound2= [];
Exp(3).hBound1=[];
Exp(3).hBound2=[];
Exp(3).CompositPlot=0;
Exp(3).Trace= []; % added for Trend BoxPlot data 17_1114
Exp(3).Trace=[]; % added for Trend BoxPlot data 17_1114
% set(handles.expName3,'string',char(Exp(expN).resDir));
end
@@ -850,7 +850,7 @@ function listboxGnOrf_Callback(hObject, eventdata, handles)
zoneSel=3;
end
%}
zoneSel= zonePB
zoneSel=zonePB
orfLstSel=get(handles.GeneOrfTog,'value')
% zoneSel=get(handles.zonePB1,'value')
expN=zoneSel;
@@ -861,7 +861,7 @@ function listboxGnOrf_Callback(hObject, eventdata, handles)
% selGnOrf=Exp(zoneSel).Dexp(DexpN).srtGnLst(usrInxSel); %selGnOrf=Exp(zoneSel).srtGnLst(usrInxSel);
listboxGnOrf=get(handles.listboxGnOrf,'string');
selGnOrf=listboxGnOrf(usrInxSel);
tempLB= str2mat(selGnOrf)
tempLB=str2mat(selGnOrf)
if isequal(tempLB(4:6),'cmp')||isequal(tempLB(3:6),'cmpG')
lstBoxCmpFlg=1;
EZlstBoxCmpExt %Added for RF composite behavior 17_1010
@@ -903,9 +903,9 @@ function GeneOrfTog_Callback(hObject, eventdata, handles)
orfLstSel=get(handles.GeneOrfTog,'value');
%zoneSel=get(handles.zonePB1,'value')
expN=zoneSel;
if zoneSel==1,DexpN= (get(handles.DN1,'value')); cmpTog= get(handles.CompositeTog1,'value'); end
if zoneSel==2,DexpN= (get(handles.DN2,'value')); cmpTog= get(handles.CompositeTog2,'value'); end
if zoneSel==3,DexpN= (get(handles.DN3,'value')); cmpTog= get(handles.CompositeTog3,'value'); end
if zoneSel==1,DexpN=(get(handles.DN1,'value')); cmpTog=get(handles.CompositeTog1,'value'); end
if zoneSel==2,DexpN=(get(handles.DN2,'value')); cmpTog=get(handles.CompositeTog2,'value'); end
if zoneSel==3,DexpN=(get(handles.DN3,'value')); cmpTog=get(handles.CompositeTog3,'value'); end
if orfLstSel==1 && cmpTog~=1
set(handles.listboxGnOrf,'value',1)
set(handles.listboxGnOrf,'string',Exp(zoneSel).Dexp(DexpN).srtOrfLst) %set(handles.listboxGnOrf,'string',Exp(zoneSel).srtOrfLst)
@@ -983,7 +983,7 @@ function printOL1_Callback(hObject, eventdata, handles)
% hObject handle to printOL1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% If Enable == 'on', executes on mouse press in 5 pixel border.
% If Enable =='on', executes on mouse press in 5 pixel border.
% Otherwise, executes on mouse press in 5 pixel border or over printol1.
global Exp
global ghandles
@@ -1035,7 +1035,7 @@ end
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- If Enable =='on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over printOL2.
ads2=1
end
@@ -1072,7 +1072,7 @@ end
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- If Enable =='on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over printOL3.
ads3=1
end
@@ -1144,7 +1144,7 @@ function PrintFont_Callback(hObject, eventdata, handles)
try
if ~isempty(Exp(4).plotPars)
default= Exp(4).plotPars;
default=Exp(4).plotPars;
else
default={'4','36','10','5'};
end
@@ -1159,7 +1159,7 @@ function PrintFont_Callback(hObject, eventdata, handles)
%{
else
default={'4','36','10','5'};
Exp(4).plotPars= default;
Exp(4).plotPars=default;
%}
end
end
@@ -1193,9 +1193,9 @@ function rawNorm_Callback(hObject, eventdata, handles)
traceN1=Exp(1).traceN;
traceN2=Exp(2).traceN;
traceN3=Exp(3).traceN;
selTrace1= Exp(1).seltraceN;
selTrace2= Exp(2).seltraceN;
selTrace3= Exp(3).seltraceN;
selTrace1=Exp(1).seltraceN;
selTrace2=Exp(2).seltraceN;
selTrace3=Exp(3).seltraceN;
dispAlg=get(handles.rawNorm,'value')
@@ -1484,7 +1484,7 @@ function HtMapTog3_Callback(hObject, eventdata, handles)
prntHt=0;
expN=3;
DexpN=Exp(3).DexpN;
resetTg= Exp(3).Dexp(DexpN).resetHtmpTg;
resetTg=Exp(3).Dexp(DexpN).resetHtmpTg;
Exp(3).htmapPBsel=Exp(3).htmapPBsel+1;
if Exp(3).htmapPBsel==resetTg, Exp(3).htmapPBsel=0; end
if Exp(3).htmapPBsel==3, set(handles.HtMapTog3,'string','N1')
@@ -1536,7 +1536,7 @@ Exp(1).traceN=0;
Exp(1).hOL =[]; Exp(1).hOLb=[];
Exp(1).hOLname={}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
Exp(1).hOLplateNum=[];
Exp(1).hOLresDir= {};
Exp(1).hOLresDir={};
set(ghandles.OLay2,'string',{''})
set(ghandles.OLexp2,'string',{''})
@@ -1545,7 +1545,7 @@ Exp(2).traceN=0;
Exp(2).hOL =[]; Exp(2).hOLb=[];
Exp(2).hOLname={}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
Exp(2).hOLplateNum=[];
Exp(2).hOLresDir= {};
Exp(2).hOLresDir={};
set(ghandles.OLay3,'string',{''})
set(ghandles.OLexp3,'string',{''})
@@ -1554,7 +1554,7 @@ Exp(3).traceN=0;
Exp(3).hOL =[]; Exp(3).hOLb=[];
Exp(3).hOLname={}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
Exp(3).hOLplateNum=[];
Exp(3).hOLresDir= {};
Exp(3).hOLresDir={};
%}
% hObject handle to quickView (see GCBO)
@@ -1583,7 +1583,7 @@ function RFtable3_Callback(hObject, eventdata, handles)
global Exp
global ghandles
expN=3;
DexpN= get(handles.DN3,'value');
DexpN=get(handles.DN3,'value');
EZtableRFdiag
end
@@ -1595,14 +1595,14 @@ function DN1_Callback(hObject, eventdata, handles)
global Exp
expN=1;
input=get(hObject,'String');
Max= Exp(expN).DexpLength;
Min= 0; %(get(handles.DN1,'min'));
if str2num(input) > Min && str2num(input) <= Max
Max=Exp(expN).DexpLength;
Min=0; %(get(handles.DN1,'min'));
if str2num(input) > Min && str2num(input) <=Max
display(input)
set(handles.DN1,'value',str2double(input));
else
if str2double(input) >= Max, set(handles.DN1,'value',Max); set(handles.DN1,'string',num2str(Max));end
if str2double(input) <= Min, set(handles.DN1,'value',Min),set(handles.DN1,'string',num2str(1));end
if str2double(input) >=Max, set(handles.DN1,'value',Max); set(handles.DN1,'string',num2str(Max));end
if str2double(input) <=Min, set(handles.DN1,'value',Min),set(handles.DN1,'string',num2str(1));end
end
EZVimDisplay
end
@@ -1621,12 +1621,12 @@ function DN2_Callback(hObject, eventdata, handles)
input=get(hObject,'String');
Max=Exp(expN).DexpLength;
Min=0; %(get(handles.DN1,'min'));
if str2num(input) > Min && str2num(input) <= Max
if str2num(input) > Min && str2num(input) <=Max
display(input)
set(handles.DN2,'value',str2double(input));
else
if str2double(input) >= Max, set(handles.DN2,'value',Max); set(handles.DN2,'string',num2str(Max));end
if str2double(input) <= Min, set(handles.DN2,'value',Min),set(handles.DN2,'string',num2str(1));end
if str2double(input) >=Max, set(handles.DN2,'value',Max); set(handles.DN2,'string',num2str(Max));end
if str2double(input) <=Min, set(handles.DN2,'value',Min),set(handles.DN2,'string',num2str(1));end
end
EZVimDisplay
end
@@ -1644,12 +1644,12 @@ function DN3_Callback(hObject, eventdata, handles)
input=get(hObject,'String');
Max=Exp(expN).DexpLength;
Min=0; % (get(handles.DN1,'min'));
if str2num(input) > Min && str2num(input) <= Max
if str2num(input) > Min && str2num(input) <=Max
display(input)
set(handles.DN3,'value',str2double(input));
else
if str2double(input) >= Max, set(handles.DN3,'value',Max); set(handles.DN3,'string',num2str(Max));end
if str2double(input) <= Min, set(handles.DN3,'value',Min),set(handles.DN3,'string',num2str(1));end
if str2double(input) >=Max, set(handles.DN3,'value',Max); set(handles.DN3,'string',num2str(Max));end
if str2double(input) <=Min, set(handles.DN3,'value',Min),set(handles.DN3,'string',num2str(1));end
end
EZVimDisplay
end
@@ -1666,7 +1666,7 @@ function CompositePB1_Callback(hObject, eventdata, handles)
global Exp
global ghandles
expN=1;
DexpN= get(handles.DN1,'value');
DexpN=get(handles.DN1,'value');
EZcompositePlot
end
@@ -1702,7 +1702,7 @@ function SpotViewInterval_Callback(hObject, eventdata, handles)
try
if ~isempty(Exp(4).SpotVIntervPar)
default= Exp(4).SpotVIntervPar;
default=Exp(4).SpotVIntervPar;
else
default={'1'};
end
@@ -1772,7 +1772,7 @@ function CompositeTog3_Callback(hObject, eventdata, handles)
ghandles=handles;
expN=3;
DexpN= (get(handles.DN3,'value'));
DexpN=(get(handles.DN3,'value'));
%set(handles.zonePB1,'value',0)
%set(handles.zonePB2,'value',0)
%set(handles.zonePB3,'value',1)
@@ -1791,17 +1791,17 @@ end
function TrendsBoxPlot_Callback(hObject, eventdata, handles)
global userPars
userPars.boxplotFlg= 1;
userPars.boxplotFlg=1;
prompt={...
'Set "Outliers" On/Off:', ...
'Set "Notch" On/Off:', ...
'Enter "LabelShift" value[default= 0.5]:', ...
'Enter "LabelShift" value[default=0.5]:', ...
'Enter "Font Size [default=8:' ...
'Enter "Label Angle" [default=45]' ...
'Enter Upper K Limit value[typical= 155]:'};
'Enter Upper K Limit value[typical=155]:'};
name='Box Plot Parameters';
numlines=1;
%defaultanswer= {'on','on','0.3','8','45'};
%defaultanswer={'on','on','0.3','8','45'};
defaultanswer=userPars.BPdefault;
answer=inputdlg(prompt,name,numlines,defaultanswer);
userPars.BPoutliers=answer(1);
@@ -1819,22 +1819,22 @@ function TrendsOverlay_Callback(hObject, eventdata, handles)
global userPars
userPars.boxplotFlg=0;
prompt={'Enter Upper K Limit value[typical= 155]:'};
prompt={'Enter Upper K Limit value[typical=155]:'};
name='Box Plot Parameters';
numlines=1;
% defaultanswer= {'1000'};
% if ~exist('userPars.Trenddefault','var'), userPars.Trenddefault= {'1000'}; end
% defaultanswer={'1000'};
% if ~exist('userPars.Trenddefault','var'), userPars.Trenddefault={'1000'}; end
defaultanswer=userPars.BPdefault(6)
% try
% defaultanswer=userPars.Trenddefault;
% catch
% userPars.Trenddefault= {'1000'}
% defaultanswer= userPars.Trenddefault;
% userPars.Trenddefault={'1000'}
% defaultanswer=userPars.Trenddefault;
% end
answer=inputdlg(prompt,name,numlines,defaultanswer);
userPars.kfiltLim= str2double(cell2mat(answer(1)));
%userPars.Trenddefault= answer(1);
userPars.BPdefault(6)= answer(1);
userPars.kfiltLim=str2double(cell2mat(answer(1)));
%userPars.Trenddefault=answer(1);
userPars.BPdefault(6)=answer(1);
end
% Executes on button press in printHt1.
@@ -1844,7 +1844,7 @@ function printHt1_Callback(hObject, eventdata, handles)
DexpN=Exp(1).DexpN;
expN=1;
prntHt=1;
htMapTogPBfg= 1;
htMapTogPBfg=1;
EZhtMap
prntHt=0;
end
@@ -1880,16 +1880,16 @@ function HMapRange_Callback(hObject, eventdata, handles)
global adj
global flip
prompt={'Enter Standard Deviation Multiplier value[typical= 2.0]:'};
% prompt={'Enter Standard Deviation Multiplier value[typical= 3.0]:','Colormap Flip[Typical=T]'};
prompt={'Enter Standard Deviation Multiplier value[typical=2.0]:'};
% prompt={'Enter Standard Deviation Multiplier value[typical=3.0]:','Colormap Flip[Typical=T]'};
name='Heatmap Adjustment range';
numlines=1;
defaultanswer= {'2.0'};
% defaultanswer= {'3.0','T'};
defaultanswer={'2.0'};
% defaultanswer={'3.0','T'};
answer=inputdlg(prompt,name,numlines,defaultanswer);
adj= str2double(answer(1));
flip= 'T';
% flip= upper(answer(2));
adj=str2double(answer(1));
flip='T';
% flip=upper(answer(2));
end
function SetExpJobsFolder_Callback(hObject, eventdata, handles)
@@ -1949,7 +1949,7 @@ function zonePB2_Callback(hObject, eventdata, handles)
zonePB=2
%if get(handles.zonePB2,'value')==0, set(handles.zonePB2,'value',1); end
set(handles.zonePB2,'value',1);
DexpN= get(handles.DN2,'value')
DexpN=get(handles.DN2,'value')
set(handles.zonePB1,'value',0);
set(handles.zonePB3,'value',0);
set(ghandles.zonePB2,'value',1);
@@ -1990,7 +1990,7 @@ function zonePB3_Callback(hObject, eventdata, handles)
global ghandles
global zonePB
zonePB= 3
zonePB=3
%if get(handles.zonePB3,'value')==0, set(handles.zonePB3,'value',1); end
set(handles.zonePB3,'value',1);
DexpN=get(handles.DN3,'value');
@@ -2035,7 +2035,7 @@ function zoneRad1_Callback(hObject, eventdata, handles)
global Exp
if get(handles.zoneRad1,'value')==0, set(handles.zoneRad1,'value',1); end
DexpN= get(handles.DN1,'value')
DexpN=get(handles.DN1,'value')
set(handles.zoneRad2,'value',0)
set(handles.zoneRad3,'value',0)
orfLstSel=get(handles.GeneOrfTog,'value')
@@ -2061,7 +2061,7 @@ function zoneRad2_Callback(hObject, eventdata, handles)
global Exp
if get(handles.zoneRad2,'value')==0, set(handles.zoneRad2,'value',1); end
DexpN= get(handles.DN2,'value')
DexpN=get(handles.DN2,'value')
set(handles.zoneRad1,'value',0)
set(handles.zoneRad3,'value',0)
@@ -2089,7 +2089,7 @@ function zoneRad3_Callback(hObject, eventdata, handles)
global Exp
if get(handles.zoneRad3,'value')==0, set(handles.zoneRad3,'value',1); end
DexpN= get(handles.DN3,'value')
DexpN=get(handles.DN3,'value')
set(handles.zoneRad1,'value',0)
set(handles.zoneRad2,'value',0)
orfLstSel=get(handles.GeneOrfTog,'value')
@@ -2120,7 +2120,7 @@ end
% handles structure with handles and user data (see GUIDATA)
% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- If Enable =='on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over printOL1.
function printOL1_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to printOL1 (see GCBO)

14
workflow/apps/matlab/ezview/EZviewInfoBox.m
View File

@@ -5,11 +5,11 @@
%load 'EZsgdInfo'
%}
text=Exp(4).SGDtext;
destPerMP= Exp(zoneSel).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
indx=((LBr-1)*24) +LBc
MP=Exp(zoneSel).Dexp(DexpN).MP;
destPerMP= Exp(zoneSel).Dexp(DexpN).destPerMP; %length(gS.DM1.drug);
pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
plateNum=(LBmp-1)*destPerMP + pertSel;
indx=((LBr-1)*24) +LBc
MP=Exp(zoneSel).Dexp(DexpN).MP;
a=[];
if get(handles.GeneOrfTog,'value')==0
gene=MP(1,LBmp).genename{1,1}(indx);
@@ -25,7 +25,6 @@ if get(handles.GeneOrfTog,'value')==0
if strcmpi(gnXref,'HO'), gene=strcat(gene,',',gnXref);end
name=strcat(char(gene),'->',char(orfXref));
end
elseif get(handles.GeneOrfTog,'value')==1
orf=MP(1,LBmp).orf{1,1}(indx);
orfLength=length(char(orf));
@@ -44,6 +43,7 @@ if isempty(a)
name='Not Found';
desc=[]; proc=[]; func=[]; loc=[];
end
%{
if get(handles.listboxGnOrf,'value')&& ~isempty(a)
desc=char(text(a,32,:));
@@ -62,4 +62,4 @@ elseif isempty(b)
desc=[]; proc=[]; func=[]; loc=[];
end
%}
hh=msgbox(sprintf('%s\n%s\n%s%s\n%s%s\n%s%s\n',name,desc,'P->',proc,'F->',func,'C->',loc),'SGD Ontology Info','replace')
hh=msgbox(sprintf('%s\n%s\n%s%s\n%s%s\n%s%s\n',name,desc,'P->',proc,'F->',func,'C->',loc),'SGD Ontology Info','replace')

373
workflow/apps/matlab/ezview/questdlgJWR.m
View File

@@ -1,5 +1,5 @@
function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
%QUESTDLG Question dialog box.
% QUESTDLG Question dialog box.
% ButtonName=QUESTDLG(Question) creates a modal dialog box that
% automatically wraps the cell array or string (vector or matrix)
% Question to fit an appropriately sized window. The name of the
@@ -60,101 +60,84 @@ function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
%
% See also DIALOG, ERRORDLG, HELPDLG, INPUTDLG, LISTDLG,
% MSGBOX, WARNDLG, FIGURE, TEXTWRAP, UIWAIT, UIRESUME.
% Copyright 1984-2010 The MathWorks, Inc.
% $Revision: 5.55.4.17 $
if nargin<1
if nargin<1
error('MATLAB:questdlg:TooFewArguments', 'Too few arguments for QUESTDLG');
end
end
Interpreter='none';
Question=dialogCellstrHelper(Question);
Interpreter='none';
Question=dialogCellstrHelper(Question);
%%%%%%%%%%%%%%%%%%%%%
%%% General Info. %%%
%%%%%%%%%%%%%%%%%%%%%
Black =[0 0 0 ]/255;
% LightGray =[192 192 192 ]/255;
% LightGray2 =[160 160 164 ]/255;
% MediumGray =[128 128 128 ]/255;
% White =[255 255 255 ]/255;
% General Information
Black =[0 0 0 ]/255;
% LightGray =[192 192 192 ]/255;
% LightGray2 =[160 160 164 ]/255;
% MediumGray =[128 128 128 ]/255;
% White =[255 255 255 ]/255;
%%%%%%%%%%%%%%%%%%%%
%%% Nargin Check %%%
%%%%%%%%%%%%%%%%%%%%
if nargout>1
% Nargin Check
if nargout>1
error('MATLAB:questdlg:WrongNumberOutputs', 'Wrong number of output arguments for QUESTDLG');
end
if nargin==1,Title=' ';end
if nargin<=2, Default='Yes';end
if nargin==3, Default=Btn1 ;end
if nargin<=3, Btn1='Yes'; Btn2='No'; Btn3='Cancel';NumButtons=3;end
if nargin==4, Default=Btn2;Btn2=[];Btn3=[];NumButtons=1;end
if nargin==5, Default=Btn3;Btn3=[];NumButtons=2;end
if nargin==6, NumButtons=3;end
if nargin>6
error('MATLAB:questdlg:TooManyInputs', 'Too many input arguments');NumButtons=3; %#ok
end
end
if isstruct(Default),
if nargin==1,Title=' ';end
if nargin<=2, Default='Yes';end
if nargin==3, Default=Btn1 ;end
if nargin<=3, Btn1='Yes'; Btn2='No'; Btn3='Cancel';NumButtons=3;end
if nargin==4, Default=Btn2;Btn2=[];Btn3=[];NumButtons=1;end
if nargin==5, Default=Btn3;Btn3=[];NumButtons=2;end
if nargin==6, NumButtons=3;end
if nargin>6
error('MATLAB:questdlg:TooManyInputs', 'Too many input arguments');NumButtons=3; %#ok
end
if isstruct(Default),
Interpreter=Default.Interpreter;
Default=Default.Default;
end
end
% Create QuestFig
FigPos=get(0,'DefaultFigurePosition');
FigPos(3)=267;
FigPos(4)=70;
FigPos=getnicedialoglocation(FigPos, get(0,'DefaultFigureUnits'));
%%%%%%%%%%%%%%%%%%%%%%%
%%% Create QuestFig %%%
%%%%%%%%%%%%%%%%%%%%%%%
FigPos =get(0,'DefaultFigurePosition');
FigPos(3)=267;
FigPos(4)= 70;
FigPos =getnicedialoglocation(FigPos, get(0,'DefaultFigureUnits'));
QuestFig=dialog( ...
'Visible' ,'off' , ...
'Name' ,Title , ...
'Pointer' ,'arrow' , ...
'Position' ,FigPos , ...
'KeyPressFcn' ,@doFigureKeyPress , ...
'IntegerHandle' ,'off' , ...
'WindowStyle' ,'normal' , ...
'HandleVisibility','callback' , ...
'CloseRequestFcn' ,@doDelete , ...
QuestFig=dialog(...
'Visible' ,'off', ...
'Name' ,Title, ...
'Pointer' ,'arrow', ...
'Position' ,FigPos, ...
'KeyPressFcn' ,@doFigureKeyPress, ...
'IntegerHandle' ,'off', ...
'WindowStyle' ,'normal', ...
'HandleVisibility','callback', ...
'CloseRequestFcn' ,@doDelete, ...
'Tag' ,Title ...
);
%%%%%%%%%%%%%%%%%%%%%
%%% Set Positions %%%
%%%%%%%%%%%%%%%%%%%%%
DefOffset =10;
IconWidth =54;
IconHeight =54;
IconXOffset=DefOffset;
IconYOffset=FigPos(4)-DefOffset-IconHeight; %#ok
IconCMap=[Black;get(QuestFig,'Color')]; %#ok
DefBtnWidth =56;
BtnHeight =22;
BtnYOffset=DefOffset;
BtnWidth=DefBtnWidth;
ExtControl=uicontrol(QuestFig , ...
% Set Positions
DefOffset =10;
IconWidth =54;
IconHeight =54;
IconXOffset=DefOffset;
IconYOffset=FigPos(4)-DefOffset-IconHeight; %#ok
IconCMap=[Black;get(QuestFig,'Color')]; %#ok
DefBtnWidth =56;
BtnHeight =22;
BtnYOffset=DefOffset;
BtnWidth=DefBtnWidth;
ExtControl=uicontrol(...
QuestFig , ...
'Style' ,'pushbutton', ...
'String' ,' ' ...
);
btnMargin=1.4;
set(ExtControl,'String',Btn1);
BtnExtent=get(ExtControl,'Extent');
BtnWidth=max(BtnWidth,BtnExtent(3)+8);
if NumButtons > 1
btnMargin=1.4;
set(ExtControl,'String',Btn1);
BtnExtent=get(ExtControl,'Extent');
BtnWidth=max(BtnWidth,BtnExtent(3)+8);
if NumButtons > 1
set(ExtControl,'String',Btn2);
BtnExtent=get(ExtControl,'Extent');
BtnWidth=max(BtnWidth,BtnExtent(3)+8);
@@ -163,49 +146,39 @@ if NumButtons > 1
BtnExtent=get(ExtControl,'Extent');
BtnWidth=max(BtnWidth,BtnExtent(3)*btnMargin);
end
end
BtnHeight=max(BtnHeight,BtnExtent(4)*btnMargin);
delete(ExtControl);
MsgTxtXOffset=IconXOffset+IconWidth;
FigPos(3)=max(FigPos(3),MsgTxtXOffset+NumButtons*(BtnWidth+2*DefOffset));
set(QuestFig,'Position',FigPos);
BtnXOffset=zeros(NumButtons,1);
if NumButtons==1,
end
BtnHeight=max(BtnHeight,BtnExtent(4)*btnMargin);
delete(ExtControl);
MsgTxtXOffset=IconXOffset+IconWidth;
FigPos(3)=max(FigPos(3),MsgTxtXOffset+NumButtons*(BtnWidth+2*DefOffset));
set(QuestFig,'Position',FigPos);
BtnXOffset=zeros(NumButtons,1);
if NumButtons==1,
BtnXOffset=(FigPos(3)-BtnWidth)/2;
elseif NumButtons==2,
BtnXOffset=[MsgTxtXOffset
FigPos(3)-DefOffset-BtnWidth];
elseif NumButtons==3,
BtnXOffset=[MsgTxtXOffset
0
FigPos(3)-DefOffset-BtnWidth];
elseif NumButtons==2,
BtnXOffset=[MsgTxtXOffset FigPos(3)-DefOffset-BtnWidth];
elseif NumButtons==3,
BtnXOffset=[MsgTxtXOffset 0 FigPos(3)-DefOffset-BtnWidth];
BtnXOffset(2)=(BtnXOffset(1)+BtnXOffset(3))/2;
end
end
MsgTxtYOffset=DefOffset+BtnYOffset+BtnHeight;
MsgTxtYOffset=DefOffset+BtnYOffset+BtnHeight;
% Calculate current msg text width and height. If negative,
% clamp it to 1 since its going to be recalculated/corrected later
% based on the actual msg string
MsgTxtWidth=max(1, FigPos(3)-DefOffset-MsgTxtXOffset-IconWidth);
MsgTxtHeight=max(1, FigPos(4)-DefOffset-MsgTxtYOffset);
% Calculate current msg text width and height. If negative,
% clamp it to 1 since its going to be recalculated/corrected later
% based on the actual msg string
MsgTxtWidth=max(1, FigPos(3)-DefOffset-MsgTxtXOffset-IconWidth);
MsgTxtHeight=max(1, FigPos(4)-DefOffset-MsgTxtYOffset);
MsgTxtForeClr=Black;
MsgTxtBackClr=get(QuestFig,'Color');
CBString='uiresume(gcbf)';
DefaultValid=false;
DefaultWasPressed=false;
BtnHandle=cell(NumButtons, 1);
DefaultButton=0;
MsgTxtForeClr=Black;
MsgTxtBackClr=get(QuestFig,'Color');
CBString='uiresume(gcbf)';
DefaultValid=false;
DefaultWasPressed=false;
BtnHandle=cell(NumButtons, 1);
DefaultButton=0;
% Check to see if the Default string passed does match one of the
% strings on the buttons in the dialog. If not, throw a warning.
for i=1:NumButtons
% Check to see if the Default string passed does match one of the
% strings on the buttons in the dialog. If not, throw a warning.
for i=1:NumButtons
switch i
case 1
ButtonString=Btn1;
@@ -214,7 +187,6 @@ for i=1:NumButtons
DefaultValid=true;
DefaultButton=1;
end
case 2
ButtonString=Btn2;
ButtonTag='Btn2';
@@ -231,41 +203,38 @@ for i=1:NumButtons
end
end
BtnHandle{i}=uicontrol(QuestFig , ...
BtnHandle{i}=uicontrol(QuestFig, ...
'Style' ,'pushbutton', ...
'Position' ,[ BtnXOffset(1) BtnYOffset BtnWidth BtnHeight ] , ...
'KeyPressFcn' ,@doControlKeyPress , ...
'Callback' ,CBString , ...
'Position' ,[ BtnXOffset(1) BtnYOffset BtnWidth BtnHeight ], ...
'KeyPressFcn' ,@doControlKeyPress, ...
'Callback' ,CBString, ...
'String' ,ButtonString, ...
'HorizontalAlignment','center' , ...
'Tag' ,ButtonTag ...
'HorizontalAlignment','center', ...
'Tag' ,ButtonTag...
);
end
end
if ~DefaultValid
if ~DefaultValid
warnstate=warning('backtrace','off');
warning('MATLAB:QUESTDLG:stringMismatch','Default string does not match any button string name.');
warning(warnstate);
end
end
MsgHandle=uicontrol(QuestFig , ...
'Style' ,'text' , ...
'Position' ,[MsgTxtXOffset MsgTxtYOffset 0.95*MsgTxtWidth MsgTxtHeight ] , ...
'String' ,{' '} , ...
'Tag' ,'Question' , ...
'HorizontalAlignment','left' , ...
'FontWeight' ,'bold' , ...
'BackgroundColor' ,MsgTxtBackClr , ...
MsgHandle=uicontrol(QuestFig, ...
'Style' ,'text', ...
'Position' ,[MsgTxtXOffset MsgTxtYOffset 0.95*MsgTxtWidth MsgTxtHeight ], ...
'String' ,{' '}, ...
'Tag' ,'Question', ...
'HorizontalAlignment','left', ...
'FontWeight' ,'bold', ...
'BackgroundColor' ,MsgTxtBackClr, ...
'ForegroundColor' ,MsgTxtForeClr ...
);
[WrapString,NewMsgTxtPos]=textwrap(MsgHandle,Question,75);
% NumLines=size(WrapString,1);
AxesHandle=axes('Parent',QuestFig,'Position',[0 0 1 1],'Visible','off');
texthandle=text( ...
[WrapString,NewMsgTxtPos]=textwrap(MsgHandle,Question,75);
% NumLines=size(WrapString,1);
AxesHandle=axes('Parent',QuestFig,'Position',[0 0 1 1],'Visible','off');
texthandle=text( ...
'Parent' ,AxesHandle , ...
'Units' ,'pixels' , ...
'Color' ,get(BtnHandle{1},'ForegroundColor') , ...
@@ -278,66 +247,52 @@ texthandle=text( ...
'Tag' ,'Question' ...
);
textExtent=get(texthandle, 'Extent');
% (g357851)textExtent and extent from uicontrol are not the same. For window, extent from uicontrol is larger
%than textExtent. But on Mac, it is reverse. Pick the max value.
MsgTxtWidth=max([MsgTxtWidth NewMsgTxtPos(3)+2 textExtent(3)]);
MsgTxtHeight=max([MsgTxtHeight NewMsgTxtPos(4)+2 textExtent(4)]);
MsgTxtXOffset=IconXOffset+IconWidth+DefOffset;
FigPos(3)=max(NumButtons*(BtnWidth+DefOffset)+DefOffset, ...
textExtent=get(texthandle, 'Extent');
% (g357851)textExtent and extent from uicontrol are not the same. For window, extent from uicontrol is larger
% than textExtent. But on Mac, it is reverse. Pick the max value.
MsgTxtWidth=max([MsgTxtWidth NewMsgTxtPos(3)+2 textExtent(3)]);
MsgTxtHeight=max([MsgTxtHeight NewMsgTxtPos(4)+2 textExtent(4)]);
MsgTxtXOffset=IconXOffset+IconWidth+DefOffset;
FigPos(3)=max(NumButtons*(BtnWidth+DefOffset)+DefOffset, ...
MsgTxtXOffset+MsgTxtWidth+DefOffset);
% Center Vertically around icon
if IconHeight>MsgTxtHeight,
% Center Vertically around icon
if IconHeight>MsgTxtHeight,
IconYOffset=BtnYOffset+BtnHeight+DefOffset;
MsgTxtYOffset=IconYOffset+(IconHeight-MsgTxtHeight)/2;
FigPos(4)=IconYOffset+IconHeight+DefOffset;
% center around text
else
% Center around text
else
MsgTxtYOffset=BtnYOffset+BtnHeight+DefOffset;
IconYOffset=MsgTxtYOffset+(MsgTxtHeight-IconHeight)/2;
FigPos(4)=MsgTxtYOffset+MsgTxtHeight+DefOffset;
end
end
if NumButtons==1,
if NumButtons==1
BtnXOffset=(FigPos(3)-BtnWidth)/2;
elseif NumButtons==2,
BtnXOffset=[(FigPos(3)-DefOffset)/2-BtnWidth
(FigPos(3)+DefOffset)/2
];
elseif NumButtons==3,
elseif NumButtons==2
BtnXOffset=[(FigPos(3)-DefOffset)/2-BtnWidth (FigPos(3)+DefOffset)/2];
elseif NumButtons==3
BtnXOffset(2)=(FigPos(3)-BtnWidth)/2;
BtnXOffset=[BtnXOffset(2)-DefOffset-BtnWidth
BtnXOffset(2)
BtnXOffset(2)+BtnWidth+DefOffset
];
end
BtnXOffset=[BtnXOffset(2)-DefOffset-BtnWidth BtnXOffset(2) BtnXOffset(2)+BtnWidth+DefOffset];
end
set(QuestFig ,'Position',getnicedialoglocation(FigPos, get(QuestFig,'Units')));
assert(iscell(BtnHandle));
BtnPos=cellfun(@(bh)get(bh,'Position'), BtnHandle, 'UniformOutput', false);
BtnPos=cat(1,BtnPos{:});
BtnPos(:,1)=BtnXOffset;
BtnPos=num2cell(BtnPos,2);
set(QuestFig ,'Position',getnicedialoglocation(FigPos, get(QuestFig,'Units')));
assert(iscell(BtnHandle));
BtnPos=cellfun(@(bh)get(bh,'Position'), BtnHandle, 'UniformOutput', false);
BtnPos=cat(1,BtnPos{:});
BtnPos(:,1)=BtnXOffset;
BtnPos=num2cell(BtnPos,2);
assert(iscell(BtnPos));
cellfun(@(bh,pos)set(bh, 'Position', pos), BtnHandle, BtnPos, 'UniformOutput', false);
assert(iscell(BtnPos));
cellfun(@(bh,pos)set(bh, 'Position', pos), BtnHandle, BtnPos, 'UniformOutput', false);
if DefaultValid
if DefaultValid
setdefaultbutton(QuestFig, BtnHandle{DefaultButton});
end
end
delete(MsgHandle);
delete(MsgHandle);
set(texthandle, 'Position',[MsgTxtXOffset MsgTxtYOffset 0]);
set(texthandle, 'Position',[MsgTxtXOffset MsgTxtYOffset 0]);
IconAxes=axes( ...
IconAxes=axes(...
'Parent' ,QuestFig , ...
'Units' ,'Pixels' , ...
'Position' ,[IconXOffset IconYOffset IconWidth IconHeight], ...
@@ -345,51 +300,47 @@ IconAxes=axes( ...
'Tag' ,'IconAxes' ...
);
set(QuestFig ,'NextPlot','add');
load dialogicons.mat questIconData questIconMap;
IconData=questIconData;
questIconMap(256,:)=get(QuestFig,'Color');
IconCMap=questIconMap;
Img=image('CData',IconData,'Parent',IconAxes);
set(QuestFig, 'Colormap', IconCMap);
set(IconAxes, ...
set(QuestFig ,'NextPlot','add');
load dialogicons.mat questIconData questIconMap;
IconData=questIconData;
questIconMap(256,:)=get(QuestFig,'Color');
IconCMap=questIconMap;
Img=image('CData',IconData,'Parent',IconAxes);
set(QuestFig, 'Colormap', IconCMap);
set(IconAxes, ...
'Visible','off' , ...
'YDir' ,'reverse' , ...
'XLim' ,get(Img,'XData'), ...
'YLim' ,get(Img,'YData') ...
);
% make sure we are on screen
movegui(QuestFig)
% Make sure we are on screen
movegui(QuestFig)
set(QuestFig ,'WindowStyle','modal','Visible','on');
drawnow;
set(QuestFig ,'WindowStyle','modal','Visible','on');
drawnow;
if DefaultButton ~= 0
if DefaultButton ~=0
uicontrol(BtnHandle{DefaultButton});
end
end
if ishghandle(QuestFig)
if ishghandle(QuestFig)
% Go into uiwait if the figure handle is still valid.
% This is mostly the case during regular use.
uiwait(QuestFig);
end
end
% Check handle validity again since we may be out of uiwait because the
% figure was deleted.
if ishghandle(QuestFig)
% Check handle validity again since we may be out of uiwait because the
% figure was deleted.
if ishghandle(QuestFig)
if DefaultWasPressed
ButtonName=Default;
else
ButtonName=get(get(QuestFig,'CurrentObject'),'String');
end
doDelete;
else
else
ButtonName='';
end
end
function doFigureKeyPress(obj, evd) %#ok
switch(evd.Key)