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hartman-server/workflow/apps/matlab/ezview/EZhtMap.m
Bryan Roessler c323eef935 Add ezview
2024-07-29 12:31:26 -04:00

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Matlab
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%EZhtMap
global Exp
global ghandles
global adj
global flip
if isempty(adj), adj=1.5; flip='T'; end
load('MyColormap1','modJet1')
load('MyColormap2','modJet2')
%load('MyColormap2','modJet0')
%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;
try
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
catch
MPsel=1;
pertSel=1;
end
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));
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)
for j=1:size(L,2)
if L(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(:));
else
L4hMap(i,j)= L(i,j);
end
end
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')
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
%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 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
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}));
title({strcat('L HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
colormap(modJet1) %Fix added 230814
%3333333333 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
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)
for j=1:size(K,2)
if K(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(:));
else
hMap(i,j)= K(i,j);
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
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})
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}));
title({strcat('K HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
%444444444 rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr
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)
for j=1:size(r,2)
if r(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(:));
else
hMap(i,j)= r(i,j);
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
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})
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}));
title({strcat('r HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
%33333333333333333333333333333333333333333333333333333(1111111111111111111)
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
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';
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
end
if RFconfig~=1,
prompt={
QctrlRF,...
QpertRF,...
};
name='Interaction User Input';
numlines=1;
answer=inputdlg(prompt,name,numlines,defaultanswer);
if RFconfig==2,
if ~ismember(answer{1},['g' 'G' 'l' 'L']), answer(1)=defaultanswer(1); end
if ~ismember(answer{2},['g' 'G' 'l' 'L']), answer(2)=defaultanswer(2); end
end
if RFconfig==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
end
end %if htMapTogPBfg==1
htMapTogPBfg=0;
answer= Exp(expN).htmapRFanswer; %ZoneRelated
%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}= [];
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;
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)));
Exp(expN).HtMpIntN2=intL; %ZoneRelated
%{
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));
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);
for i=1:384
%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
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
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,:};
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;
h=image(cleanPallet);
else
figure
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 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})
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}));
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)
elseif htTog==4
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}= [];
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
I=reshape(intL,24,16);
if prntHt== 0
hTogHt= figure;
h=image(cleanPallet);
elsef
figure
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 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})
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}));
title({strcat('N2 HeatMap for - ',expLblHtmap),strcat('MP=',num2str(mpSel),' ,DM=',num2str(dmSel),mediaLBhtmap)})
end
end %if htTog==
prntHt= 0;
%************* *****
EZhtMapText %* Update htMapText for location on the first 'roll thru of htMapPB
%************* *****
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