server-scripts/qhtcp-workflow/apps/matlab/ezview/EZhtMap.m

%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

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)
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
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
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
  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];
  % 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;
  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

  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
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);
  elseif
    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

prntHt=0;

% Update htMapText for location on the first 'roll thru of htMapPB
EZhtMapText