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hartman-server/workflow/apps/matlab/ezview/EZexpSel.m
Bryan Roessler 78f33a0120 First EZview test
2024-07-29 17:26:51 -04:00

1370 lines
55 KiB
Matlab
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%EZexpSel.m %modified to accomodate App Designer issues 230829
%Called from EZviewGui.m or EZviewGui_export.m or migrapted EZviewGui_App.wlapp 230831
%{
>EZexpSel
>EZVimDisplay
>EZhtMap
>EZdiagRFsSheet
>EZsingleExUserRF
>EZmultigeneRFsLst
>EZdiagRFsSheet
>EZhtMap
>EZmultiDayGui
>EZmultiDay
>EZmultiExLoad
%}
global Expaa
global Expbb
global expType
global usrExpJobsDir
global zonePB
% Initialize some variables from matlab
ezPath=which(mfilename);
[ezDir,ezFileName]=fileparts(ezPath);
ezDir=fullfile(easyDir);
[parentDir, ~]=fileparts(ezDir);
parentDir=fullfile(parentDir); % ../easy/apps
debug=1;
if debug
disp('Running in debug mode');
disp('Initialized variables:');
whos;
end
% Set scansDir (project scans directory) intelligently
if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
scansDir=getenv('PROJECT');
fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
disp('This usually indicates that we are in standalone mode');
elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
scansDir=getenv('PROJECT_SCANS_DIR');
fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
disp('This usually indicates that we are in module mode');
else
% TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
% when changing EASY and other variables in the parent script
fprintf('Beginning parent scans directory search\n');
fprintf('This usually indicates that we are in stand-alone mode without PROJECT or PROJECT_SCANS_DIR environment variables\n');
dirsToScan={
fullfile(parentDir,'..', '..', 'scans'),
fullfile(parentDir, '..', '..', 'ExpJobs'),
fullfile('/mnt/data/scans'),
fullfile('/mnt/data/ExpJobs'),
fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
};
for d=dirsToScan
if exist(d, 'dir')
subDirs=dir(d);
if ~isempty(subDirs)
fprintf('Found a non-empty parent scans directory in our list: %s\n', d);
fprintf('Scanning inside for a project scan directory\n');
[~, sortedIndices]=sort(datenum({dirs.date}), 'descend'); % sort by newest first
sortedDirs=dirs{sortedIndices};
scansDir=sortedDirs{1};
fprintf('Selected newest project scans directory: %s\n', scansDir);
end
end
end
end
% User sanity check and warning
if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
if ~equal(getenv('PROJECT_USER'), userName)
disp("WARNING: PROJECT_USER does not match the current namespace");
end
end
% Allow module to override hardcoded default EZview directory
if exist('EZVIEW_DIR','var') && ~isempty(getenv('EZVIEW_DIR'))
EZVIEW_DIR=fullfile(getenv('EZVIEW_DIR'));
if ~strcmp(ezDir, EZVIEW_DIR) % sanity check
disp("WARNING: EZVIEW_DIR does not match this script's hardcoded EZview location");
disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
ezDir=EZVIEW_DIR;
end
fprintf('Using EZview script directory: %s from environment variable EZVIEW_DIR\n', ezDir);
else
fprintf('Using EZview script directory: %s from hardcoded default\n', ezDir);
end
w=pwd;
% Single Exp or Chronological Study
% Construct a questdlg with three options
Exp(expN).expLoadCnt= 0;
% Initiation for composite plotting cPlots
Exp(expN).cTraceN= 1;
Exp(expN).cTraceIndx= 1;
Exp(expN).CompositPlot= 0;
choice='Cancel';
expType=0;
choice=questdlg('Choose Single Exp, Chronological Study OR Multi Exp', ...
'Experiment Type Menu', ...
'Single Exp','Chronological Study','Multi Exp','Single Exp');
% Handle response
switch choice
case 'Single Exp'
disp([choice 'Single Exp Selected'])
expType=1;
case 'Chronological Study'
disp([choice 'Chronological Study Selected'])
expType=2;
case 'Multi Exp'
disp([choice 'Multi Exp Selected'])
expType=3;
case 'Cancel'
disp('Cancel Load Exp')
expType=0
end
fprintf('expType=%d\n',expType);
if expType==0, return; end
zonePB=expN;
% Pre Load setup incase failure to Load occurs
% updated 230818 to migrate to AppDesigner
if expN==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]);
end
if expN==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]);
end
if expN==3
set(handles.zonePB3,'value',1);
set(handles.zonePB1,'value',0);
set(handles.zonePB2,'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]);
end
Exp(expN).htmapRFanswer= {'G','L'}; %ZoneData
if expType==1
Exp(expN).DexpType= 'single';
% 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
% TODO don't want to cd here
try
cd(usrExpJobsDir);
catch
if ispc
cd(fullfile('C:\')); %end % \Easy\Experiments'));
else
cd(fullfile('/mnt/data/scans'))
end
end
datacursormode off;
if ispc
try
cd(usrExpJobsDir);
catch
cd(fullfile('C:\')); %end % \Easy\Experiments'));
end
else
try
cd(usrExpJobsDir);
catch
cd(fullfile('~'));
end
end
try
[openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
catch ME
catchissue='Ln50'
ME
cd(w)
return
end
%Return without execution if user cancels or doesn't select a .mat file
try
if openExpfile==0 || openExppath==0, cd(w), return, end
catch
end
if expN==1
orfLstSel=get(handles.GeneOrfTog,'value')
end
if expN==2
orfLstSel=get(handles.GeneOrfTog,'value')
end
if expN==3
orfLstSel=get(handles.GeneOrfTog,'value')
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 230906
set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
%try
ExpOutmat= fullfile(openExppath,openExpfile);
load(ExpOutmat);
cd(openExppath)
cd ..;
resDir=pwd;
Exp(expN).Dexp(1).resDir=resDir;
cd ..;
try %This try-catch is to go up one more dir if the images aren't found (from /OtherResults)
test4imageDir= imread(fullfile(pwd,'1','1.bmp'));
ExpPath=pwd;
Exp(expN).Dexp(1).ExpFoldr=ExpPath;
catch
try
cd ..
test4imageDir= imread(fullfile(pwd,'1','1.bmp'));
ExpPath=pwd;
Exp(expN).Dexp(1).ExpFoldr=ExpPath;
catch
cd(w)
end
end
cd(w)
%Experiment LOADs
%load (fullfile(ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
load (fullfile(Exp(expN).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
load(fullfile(resDir,'Fotos','Coordinates'))
load(fullfile(resDir,'Fotos','anlZones'))
load(fullfile(resDir,'Fotos','BGatTpts'))
load(fullfile(resDir,'PTmats','NImParameters'))
%Backup for cond. sothat failure to load is recovered back prev. ExpJob data
%test in temp
Exp(expN).Dexp(1).temp.DM=DM;
Exp(expN).Dexp(1).temp.MP=MP;
Exp(expN).Dexp(1).temp.scan=scan;
Exp(expN).Dexp(1).temp.FexpScanSpots=FexpScanSpots;
Exp(expN).Dexp(1).temp.FexpScanBMtp=FexpScanBMtp;
Exp(expN).Dexp(1).temp.anlZoneRefs=anlZoneRefs;
Exp(expN).Dexp(1).temp.ImParMat=ImParMat;
Exp(expN).Dexp(1).DM=Exp(expN).Dexp(1).temp.DM;
Exp(expN).Dexp(1).MP= Exp(expN).Dexp(1).temp.MP;
Exp(expN).Dexp(1).scan= Exp(expN).Dexp(1).temp.scan;
Exp(expN).Dexp(1).FexpScanSpots= Exp(expN).Dexp(1).temp.FexpScanSpots;
Exp(expN).Dexp(1).FexpScanBMtp= Exp(expN).Dexp(1).temp.FexpScanBMtp;
Exp(expN).Dexp(1).anlZoneRefs=Exp(expN).Dexp(1).temp.anlZoneRefs;
Exp(expN).Dexp(1).ImParMat=Exp(expN).Dexp(1).temp.ImParMat;
Exp(expN).DexpLength= 1;
Exp(expN).Dexp((Exp(expN).DexpLength+1):end)= [];
% Load new ExpJob
if expN==1,
% Exp(1).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr1,'max',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+.1)
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/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)
end
if expN==2,
%Exp(2).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr2,'max',length(MP));
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)
DMnum= length(Exp(expN).Dexp(1).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/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)
end
if expN==3,
%Exp(3).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr3,'max',length(MP));
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/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',{''});
set(handles.graphStrLoc1,'string',{''});
cla(handles.Paxes1)
end
if expN==2,set(handles.GeneOrfLoc2,'string',{''});
set(handles.graphStrLoc2,'string',{''});
cla(handles.Paxes2)
end
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,'string',Exp(expN).Dexp(1).srtGnLst)
set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtOrfLst)
EZVimDisplay
% Capture Exp Name
try
xp=char(Exp(expN).Dexp(1).resDir);
if ispc,
slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'\');
else
slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'/');
end
startPos=slashPos(length(slashPos)-2) +1;
endPos=(slashPos(length(slashPos)) -1);
expStrn= xp(startPos:end);
if expN==1,set(handles.expName1,'string',expStrn);end
if expN==2,set(handles.expName2,'string',expStrn);end
if expN==3,set(handles.expName3,'string',expStrn);end
catch
catchissue='Ln198'
end % nested try-catch-end
% Compile GeneList and OrfList
% Sort and add the medians of Ref Plates if RF1,RF2 exist
% Added 17-1023 For User Addition of Gene Composites to ListBox
Expaa{expN,1}= []; Expbb{expN,1}= [];
lstindx=0;
lstindxOrf=0;
spN=0;
rfcnt=0;
dRF1indx=0;
RF1mp=[]; RF2mp=[];
for mp=1:MPnum %length(Exp(expN).Dexp(1).MP)
for ind384=1:384
spN=spN+1;
try % Temp find data error
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(1).MP(mp).genename{1}(ind384))==38991,
Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={'OCT1_'};
elseif isnumeric(cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={' '};
end
%****Check for full(384spot) Reference Plates (RF1 or/and RF2)**************
RF1fullPlate=0;
try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
RF2fullPlate=0;
try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))),'blank'))... %'\<blank\>'
&& ~isnumeric(Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'')...
&& ~isempty((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))...
&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF1'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1'))... %&& mp==1)...
&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& mp==length(Exp(expN).Dexp(1).MP))...
&& iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))
lstindxOrf=lstindxOrf+1;
Exp(expN).Dexp(1).MP(mp).orf{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),':',' ');
bb(lstindxOrf,1)= (Exp(expN).Dexp(1).MP(mp).orf{1}(ind384));
bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
bb(lstindxOrf,3)={mp};
bb(lstindxOrf,4)={r};
bb(lstindxOrf,5)={c};
mutorfs(lstindxOrf)=spN; %16_0318 added for Interaction EZinteract
%Exp(expN).Dexp(1).mutSpotIndx(lstindxOrf)=spN; %16_0318 added for Interaction EZinteract
end
if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))... %'\<blank\>'
&& ~isnumeric(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'')...
&& ~isempty((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))...
&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1'))... %&& ~RF1fullPlate)...
&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& ~RF2fullPlate)...
&& iscellstr((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
lstindx=lstindx+1;
Exp(expN).Dexp(1).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
aa(lstindx,1)= (Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
aa(lstindx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
aa(lstindx,3)={mp};
aa(lstindx,4)={r};
aa(lstindx,5)={c};
mutgenes(lstindx)=spN;
elseif (RF1fullPlate==1 ||... %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384 || ...
(((length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp==1 ) && ... %(isequal((Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(1).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
~exist('RF1scanN','var')))
rfcnt=rfcnt+1;
RFs(spN:spN+383)= spN:spN+383;
RF1mp=mp
RF1scanN=(mp*DMnum)-(DMnum-1)
elseif (RF2fullPlate==1||... %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))==384 ||...
(((length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp== MPnum ) && ...
~exist('RF2scanN','var')))
rfcnt=rfcnt+1;
RFs(spN:spN+383)= spN:spN+383;
RF2mp=mp
RF2scanN= (mp*DMnum)-(DMnum-1)
%Dispersed Reference capture and find Medians
elseif strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1') && ...
(RF1fullPlate~=1)
dRF1indx=dRF1indx+1;
Exp(expN).Dexp(1).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)= (Exp(expN).Dexp(1).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;
end %if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...
%*******************************************************************************
catch
error='EZexpSel lineAfter 236 EZexpSel.m'
mp
ind384
msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
end
end %end associated with for ind384=1:384
mp
end %end associated with for mp=1:length(Exp(expN).Dexp(1).MP)
%*****************************************************
%Cover case if mutorfs RFs are labeled RF1 or RF2
try
Exp(expN).Dexp(1).mutSpotIndx.wRFs= union(RFs, mutorfs);
catch
msg= 'No RFs Found in Exp! wRFs'
Exp(expN).Dexp(1).mutSpotIndx.wRFs= mutorfs;
end
try
Exp(expN).Dexp(1).mutSpotIndx.woRFs= setdiff(mutorfs,RFs);
catch
Exp(expN).Dexp(1).mutSpotIndx.woRFs= mutorfs;
msg= 'No RFs Found in Exp! woRFs'
end
%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
Exp(expN).Dexp(1).RFmd1indx=[];
Exp(expN).Dexp(1).RFmd1LB= {[]};
Exp(expN).Dexp(1).RFmd1pltN={};
Exp(expN).Dexp(1).RFmd1val= [];
Exp(expN).Dexp(1).mean1= [];
Exp(expN).Dexp(1).std1= [];
Exp(expN).Dexp(1).min1= [];
Exp(expN).Dexp(1).max1= [];
Exp(expN).Dexp(1).RFcmpK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmd2indx= [];
Exp(expN).Dexp(1).RFmd2LB= {[]};
Exp(expN).Dexp(1).RFmd2pltN= {};
Exp(expN).Dexp(1).RFmd2val= [];
Exp(expN).Dexp(1).mean2= [];
Exp(expN).Dexp(1).std2= [];
Exp(expN).Dexp(1).min2= [];
Exp(expN).Dexp(1).max2= [];
Exp(expN).Dexp(1).RFmean= [];
Exp(expN).Dexp(1).RFstd= [];
Exp(expN).Dexp(1).RFmin= [];
Exp(expN).Dexp(1).RFmax= [];
Exp(expN).Dexp(1).RFmdPLvals= []; %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdPLB= {[]};
Exp(expN).Dexp(1).RFmdPindx= [];
Exp(expN).Dexp(1).RFmdPpltN= [];
Exp(expN).Dexp(1).RFmdPscanN= [];
Exp(expN).Dexp(1).RFmedianP= [];
Exp(expN).Dexp(1).stdP= [];
Exp(expN).Dexp(1).meanP= [];
Exp(expN).Dexp(1).minP= [];
Exp(expN).Dexp(1).maxP= [];
Exp(expN).Dexp(1).RFcmpPK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpPr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpPL= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmdGLB= {[]};
Exp(expN).Dexp(1).RFmdGindx= [];
Exp(expN).Dexp(1).RFmdGpltN= [];
Exp(expN).Dexp(1).RFmdGscanN= [];
Exp(expN).Dexp(1).RFmedianG= [];
Exp(expN).Dexp(1).RFmeanG= [];
Exp(expN).Dexp(1).RFstdG= [];
Exp(expN).Dexp(1).RFminG= [];
Exp(expN).Dexp(1).RFmaxG= [];
Exp(expN).Dexp(1).RFcmpGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGL= []; %For Ref Composite 17_1009
%{
Exp(expN).Dexp(1).RFmeanGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFstdGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFminGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmaxGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmeanGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFstdGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFminGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmaxGr= []; %For Ref Composite 17_1009
%}
if exist('RF1scanN','var')
for d=0:(DMnum-1)
medianIndx=[];
nonZeroIndx=[];
medValList=[];
rf1scN=RF1scanN+d;
try %if RF1scanN doesn't exist this addition to list will be skipped
nonZeroIndx= find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
if isempty(nonZeroIndx), nonZeroCnt=0; medianIndx= nonZeroIndx;
else nonZeroCnt=length(nonZeroIndx);
end
%
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx= nonZeroIndx(1:nonZeroCnt-1); end
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx= nonZeroIndx; end
clear medValLst
clear kValLst
clear rValLst
if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5);
medValList1{d+1}= medValLst;
min1= min(medValLst);
max1= max(medValLst);
std1= std(medValLst);
mean1= mean(medValLst);
kValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,3); %For Ref Composite 17_1009
rValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,4); %For Ref Composite 17_1009
mval1=median(medValLst); %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
RFmd1pos=find(mval1==(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5)));
RFmd1loc(1)= ceil(RFmd1pos/24); %calc r value
RFmd1loc(2)= RFmd1pos - ((RFmd1loc(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1md(',num2str(d+1),')')}; %{'RF1md'};
aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
bb(lstindxOrf,1)= {strcat('RF1md(',num2str(d+1),')')}; %{'RF1md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
%Composite Reference Amalgum Plot *********************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1cmp(',num2str(d+1),')')};
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF1cmp(',num2str(d+1),')')};
bb(lstindxOrf,2)={''};
%*******************************************************
Exp(expN).Dexp(1).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmd1indx(d+1)= RFmd1pos;
Exp(expN).Dexp(1).RFmd1pltN= RF1mp;
Exp(expN).Dexp(1).RFmd1val(d+1)= mval1;
Exp(expN).Dexp(1).RFmd1Lvals= medValLst; %17_1201 TrendOL
Exp(expN).Dexp(1).mean1(d+1)= mean1;
Exp(expN).Dexp(1).std1(d+1)= std1;
Exp(expN).Dexp(1).min1(d+1)= min1;
Exp(expN).Dexp(1).max1(d+1)= max1;
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).Lvals= medValLst; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).med= median(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).mean= mean(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).std= std(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).min= min(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).max= max(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).Kvals= kValLst; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).med= median(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).mean= mean(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).std= std(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).min= min(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).max= max(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).rvals= rValLst; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).med= median(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).mean= mean(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).std= std(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).min= min(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009
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
medianCalcFailed= 'To Few nonZero spots for valid median RF1 selection'
firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
Exp(expN).Dexp(1).RFmd1pltN= RF1mp;
try medValList1{d+1}= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt;
catch, catcherror = 'Ln356',
end
end %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
catch %try ~ln375
medianCalcTryFailed1= 'Failed! Failed! Ln362 But process continued with bogus P1ind384 spot value!'
try
firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
catch
catchissue='Ln366'
Exp(expN).Dexp(1).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(1).RFmd1pltN= RF1mp;
catch
catchissue='Ln372'
Exp(expN).Dexp(1).RFmd1pltN= 1;
end
error='EZexpSel lineAfter 258'
end %try ~ln375
end %for d=0:DMnum
end % if exist('RF1scanN','var')
%**********************************************************************************
%Calc RF2 median if a full plate of RF2s exist**************************
Exp(expN).Dexp(1).RFmd2indx=[];
Exp(expN).Dexp(1).RFmd2pltN=[];
if exist('RF2scanN','var')
for d=0:(DMnum-1)
medianIndx2=[];
nonZeroIndx2=[];
medValList2=[];
rf2scN=RF2scanN+d;
try %if RF2scanN doesn't exist this addition to list will be skipped
nonZeroIndx2= find(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5));
if isempty(nonZeroIndx2), nonZeroCnt2=0; medianIndx2= nonZeroIndx2;
else nonZeroCnt2=length(nonZeroIndx2);
end
%
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2= nonZeroIndx2(1:nonZeroCnt2-1); end
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2= nonZeroIndx2; end
clear medValLst2
clear kValLst2
clear rValLst2
if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);
medValList2{d+1}= medValLst2;
min2= min(medValLst2);
max2= max(medValLst2);
std2= std(medValLst2);
mean2= mean(medValLst2);
kValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,3); %For Ref Composite 17_1009
rValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,4); %For Ref Composite 17_1009
mval2=median(medValLst2); %mval2=median(Exp(expN).Dexp(1).scan(RF2mps).plate(1).CFout(1:383,5));
RFmd2pos=find(mval2==(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5)));
RFmd2loc(1)= ceil(RFmd2pos/24); %calc r value
RFmd2loc(2)= RFmd2pos - ((RFmd2loc(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2md(',num2str(d+1),')')}; %{'RF2md'};
aa(lstindx,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)= {strcat('RF2md(',num2str(d+1),')')}; %{'RF2md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,'std_',num2str(std2))};
%Composite Reference Amalgum Plot (CRAP)
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2cmp(',num2str(d+1),')')};
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF2cmp(',num2str(d+1),')')};
bb(lstindxOrf,2)={''};
Exp(expN).Dexp(1).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
Exp(expN).Dexp(1).RFmd2pltN= RF2mp;
Exp(expN).Dexp(1).RFmd2val(d+1)= mval2;
Exp(expN).Dexp(1).RFmd1Lvals= medValLst2; %17_1201 TrendOL
Exp(expN).Dexp(1).mean2(d+1)= mean2;
Exp(expN).Dexp(1).std2(d+1)= std2;
Exp(expN).Dexp(1).min2(d+1)= min2;
Exp(expN).Dexp(1).max2(d+1)= max2;
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).Lvals= medValLst2; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).med= median(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).mean= mean(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).std= std(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).min= min(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).max= max(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).Kvals= kValLst2; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).med= median(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).mean= mean(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).std= std(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).min= min(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).max= max(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).rvals= rValLst2; %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).med= median(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).mean= mean(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).std= std(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).min= min(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009
else
% Pick the first spot with zeros
% Use that position to satisfy and keep process OK
medianCalcFailed2= 'Too Few nonZero spots for valid median RF2 selection'
firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
Exp(expN).Dexp(1).RFmd2pltN= RF2mp;
try medValList2{d+1}= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5); nonZeroCnt2; catch, catchissue='Ln431', end
end
catch
medianCalcTryFailed2= 'Failed! Failed! Ln436 No RF1median But process continued with bogus P1ind384 spot value!'
try
firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first');
Exp(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
catch
catchissue='Ln442'
Exp(expN).Dexp(1).RFmd2indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(1).RFmd2pltN= RF2mp;
catch
catchissue='Ln448'
Exp(expN).Dexp(1).RFmd2pltN= 1;
end
error='EZexpSel lineAfter 279'
end %if RF2scanN doesn't exist this addition to list will be skipped
clear RFcombValList
RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
Exp(expN).Dexp(1).RFmean(d+1)= mean(RFcombValList);
Exp(expN).Dexp(1).RFstd(d+1)=std(RFcombValList);
try, Exp(expN).Dexp(1).RFmin(d+1)=min(RFcombValList);
catch, Exp(expN).Dexp(1).RFmin(d+1)= 0; end
try, Exp(expN).Dexp(1).RFmax(d+1)=max(RFcombValList);
catch, Exp(expN).Dexp(1).RFmax(d+1)= 0; end
end %for d=0:DMnum ln446
elseif exist('RF1scanN','var')
Exp(expN).Dexp(1).RFmean= Exp(expN).Dexp(1).mean1;
Exp(expN).Dexp(1).RFstd= Exp(expN).Dexp(1).std1;
Exp(expN).Dexp(1).RFmin= Exp(expN).Dexp(1).min1;
Exp(expN).Dexp(1).RFmax= Exp(expN).Dexp(1).max1;
end %if exist('RF2scanN','var') ln445
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%*************************************************************************************************
%***********DISPERSE REFERENCE PLATES
Exp(expN).Dexp(1).RFmdPindx=[];
Exp(expN).Dexp(1).RFmdPpltN=[];
if exist('drf','var')
%Det. index of change from one MP to the next
i=2;
chgIndx(1)=1;
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
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)));
%*****************************************
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(1).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
%vv= Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
%For Global Ref Composite 17_1009 %**************************************************************************
vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
%*****************************************************************************************************
nonZeroValsP= nonzeros(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp= std(nonZeroValsP);
mean1Disp= mean(nonZeroValsP);
minDisp= min(nonZeroValsP);
maxDisp= max(nonZeroValsP);
drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
%MEDIAN Determination for PLATES with Dispersed RFs
%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(1).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(1).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
%medValList1Disp{d}= medValLstDisp;
mval1Disp=median(medValLstDisp); %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); %(Exp(expN).Dexp(1).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(1).RFmdPLvals(d,dMPs(mm))= mval1Disp; %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))= RFmd1posD;
Exp(expN).Dexp(1).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(1).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
Exp(expN).Dexp(1).RFmedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(1).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(1).meanP(d,dMPs(mm))= mean1Disp;
Exp(expN).Dexp(1).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(1).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(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroD;
Exp(expN).Dexp(1).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(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
catch
catchissue='try at Ln565'
Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(1).RFmdPpltN= dMPs(mm);
catch
catchissue='Ln619'
Exp(expN).Dexp(1).RFmdPpltN= 1; %This might keep from breaking BUT ???
end
error='EZexpSel lineAfter 565'
end %try ~ln565
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
medianIndxG=[];
NZrfIndxG=[];
minG = min(nonzeros(vv(:,d)));
maxG = max(nonzeros(vv(:,d)));
RFmeanG= mean(nonzeros(vv(:,d)));
RFstdG= std(nonzeros(vv(:,d)));
NZrfIndxG= find(vv(:,d)); %find(nonzeros(vv(:,d))); WWRONG FOR A WHILE!
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)));
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))};
%Composite Reference Amalgum Plot ******************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RFcmpG(',num2str(d),')')};
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RFcmpG(',num2str(d),')')};
bb(lstindxOrf,2)={''};
%*****************************************************
%Exp(expN).Dexp(1).RFmdGLvals= vv(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmdGindx(d)= nzPosIndxDG;
Exp(expN).Dexp(1).RFmdGpltN(d)= RFmdDGloc(d,1);
Exp(expN).Dexp(1).RFmdGscanN(d)= uu(nzPosIndxDG,4);
Exp(expN).Dexp(1).RFmedianG(d)= mvalsDG;
Exp(expN).Dexp(1).RFminG(d)= minG;
Exp(expN).Dexp(1).RFmaxG(d)= maxG;
Exp(expN).Dexp(1).RFstdG(d)= RFstdG;
Exp(expN).Dexp(1).RFmeanG(d)= RFmeanG;
Exp(expN).Dexp(1).RFcmpGL.dm(d).Lvals= vv(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGL.dm(d).med= median(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGL.dm(d).mean= mean(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGL.dm(d).std= std(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGL.dm(d).min= min(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGL.dm(d).max= max(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).Kvals= vvK(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGK.dm(d).med= median(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).mean= mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).std= std(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).min= min(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).max= max(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).rvals= vvr(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGr.dm(d).med= median(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).mean= mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).std= std(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).min= min(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).max= max(vvr(medianIndxD,d)); %For Ref Composite 17_1009
end %if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15%
end
end % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
%*********************************************************************
%Added 17-1023 For User Addition of Gene Composites to ListBox
%Expaa{ic,1}= aa; Expbb{ic,1}= bb;
%**********************************************************************
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%try
for mp=1:MPnum %length(Exp(expN).Dexp(1).MP)
for ind384=1:384
spN=spN+1;
end
%catch
%end %try for user selected Reference routine
end
%****************************************************************************************************
gnLstRaw= strcat(aa(:,1),aa(:,2));
Exp(expN).Dexp(1).srtGnLst= sort(gnLstRaw);
orfLstRaw=strcat(bb(:,1),bb(:,2));
Exp(expN).Dexp(1).srtOrfLst= sort(orfLstRaw);
%********Auto select Zone and load listboxGnOrf data**********
zeroCLn= zeros(1,DMnum);
Exp(expN).expLoadCnt= Exp(expN).expLoadCnt+1; expLdCnt= Exp(expN).expLoadCnt;
zonePB= expN;
if expN==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(1).srtOrfLst)
else
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
end
DNLaxes1= handles.DNLaxes1; %ZoneRelated
Exp(1).hzeroCLn(expLdCnt) = plot(DNLaxes1,zeroCLn,1:DMnum,'y');
end
if expN==2
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');
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; %ZoneRelated
Exp(2).hzeroCLn(expLdCnt) = plot(DNLaxes2,zeroCLn,1:DMnum,'y');
end
if expN==3
set(handles.zonePB1,'value',0)
set(handles.zonePB2,'value',0)
set(handles.zonePB3,'value',1)
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(1).srtOrfLst)
else
set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
end
DNLaxes3= handles.DNLaxes3; %ZoneRelated
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
for i=1:Exp(expN).expLoadCnt,
try set(Exp(expN).hzeroCLn(i),'visible','off');
catch
catchissue= strcat('Ln521',i)
end,
end %ZoneRelated
end
%*********************************************************
EZdiagRFsSheet %**
%*****************
%*********************************************************
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(1).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
isempty(Exp(expN).Dexp(1).RFmeanG)
RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))==0 ||...
isempty(Exp(expN).Dexp(1).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
~isempty(Exp(expN).Dexp(1).RFmeanG)
RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
~isempty(Exp(expN).Dexp(1).RFmean)&&...
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
~isempty(Exp(expN).Dexp(1).RFmeanG)
RFconfig=3;
end
Exp(expN).RFconfig= RFconfig; %ZoneRelated
%******************************************
if RFconfig~=0
Exp(expN).Dexp(1).RFrnames=rnames;
Exp(expN).Dexp(1).RFdata= data;
Exp(expN).Dexp(1).resetHtmpTg =5; %ZoneRelated
% HtMapTog 'string', 'Current user L/N' selection'
Exp(expN).Dexp(1).spotIndx= [];
if expN==1,
Exp(1).htmapPBsel=0;
set(handles.HtMapTog1,'string','L')
%*********
EZhtMap %*
%*********
end
if expN==2,
Exp(2).htmapPBsel=0;
set(handles.HtMapTog2,'string','L')
%*********
EZhtMap %*
%*********
end
if expN==3,
Exp(3).htmapPBsel=0;
set(handles.HtMapTog3,'string','L')
%*********
EZhtMap %*
%*********
end
htMapTogPBfg=0;
elseif RFconfig==0,
RFconfigMsg= 'No RF1 references in this Experiment Job'
try
%*********************
EZsingleExUserRF
%EZmultiDayGui %*
%cd(w) %*
%EZmultiDay %*
%EZmultiExLoad %*
%*********************
catch
RFconfigMsg= 'No RF1 or User selected references in this Experiment Job'
Exp(expN).Dexp(1).resetHtmpTg =3; %ZoneRelated
end
% Exp(expN).Dexp(1).resetHtmpTg =3; %ZoneRelated
end
%*****************************************
%**********************************************
%{
try msgBadGeneName, catch, end
try
if RFconfig==0,
RFconfigMsg= 'No RF1 references in this Experiment Job'
Exp(expN).Dexp(1).resetHtmpTg =3; %ZoneRelated
end
catch
end
%***************************
%}
%*******************************************************************
elseif expType==2 %Multiple Experiment from in one Folder extraction
Exp(expN).DexpType= 'chrono';
%*********************
%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
%*************************************************
ww=pwd;
try EZmultiDayGui; catch ME
msg = ME.message, cd(ww); end %* %*
try EZmultiDay; catch ME
msg = ME.message, cd(ww); end %*
try EZmultiExLoad; catch ME
msg = ME.message, cd(ww); end %*
%*********************
elseif expType==3
Exp(expN).DexpType= 'multi';
%*********************
%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
%*************************************************
ww=pwd;
try EZmultiDayGui; catch ME
msg = ME.message,cd(ww); end %* %*
try EZmultiDay; catch ME
msg = ME.message, cd(ww); end %*
try EZmultiExLoad; catch ME
msg = ME.message, cd(ww); end %*
%*********************
else
disp('Cancel Load Exp')
end
%__________________________________________________________________________
%Bone Yard***********************************
%Exp(expN).Dexp(1).RF1cmpK.[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1)RF1cmpr= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF2cmpr= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2r= []; %For Ref Composite 17_1009
%kValList1{d+1}= kValLst; %For Ref Composite 17_1009
%kmin1= min(kValLst); %For Ref Composite 17_1009
%kmax1= max(kValLst); %For Ref Composite 17_1009
%kstd1= std(kValLst); %For Ref Composite 17_1009
%kmean1= mean(kValLst); %For Ref Composite 17_1009
%rValList1{d+1}= rValLst; %For Ref Composite 17_1009
%rmin1= min(rValLst); %For Ref Composite 17_1009
%rmax1= max(rValLst); %For Ref Composite 17_1009
%rstd1= std(rValLst); %For Ref Composite 17_1009
%rmean1= mean(rValLst); %For Ref Composite 17_1009
%kValList2{d+1}= kValLst2; %For Ref Composite 17_1009
%kmin2= min(kValLst2); %For Ref Composite 17_1009
%kmax2= max(kValLst2); %For Ref Composite 17_1009
%kstd2= std(kValLst2); %For Ref Composite 17_1009
%kmean2= mean(kValLst2); %For Ref Composite 17_1009
%rValList2{d+1}= rValLst2; %For Ref Composite 17_1009
% rmin2= min(rValLst2); %For Ref Composite 17_1009
%rmax2= max(rValLst2); %For Ref Composite 17_1009
%rstd2= std(rValLst2); %For Ref Composite 17_1009
%rmean2= mean(rValLst2); %For Ref Composite 17_1009
%{
%User Reference Input Dialog Box used in the multiExperiment Chrono setup
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);
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%First user input prototype code
if ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
prompt = {'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
'Enter GeneName of Your Reference:'};
dlg_title = 'User Reference Input';
num_lines = 1;
def = {'Ref MP(s)','USRrefGeneName'};
answer = inputdlg(prompt,dlg_title,num_lines,def);
rfMPstr= cell2mat(answer(1));
rfMPcomas=strfind((cell2mat(answer(1))),',');
n=0;
if isempty(rfMPcomas)|| max(rfMPcomas)== length(rfMPstr)
usrMPs= rfMPstr
else
for i= rfMPcomas,
n=n+1
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);
end
%}
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