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

%EZfigTrendOL.m  called from EZviewGui.m LKrTog__ Callback
%Uses data stored from OLay ; Clearing OLay clears data used by this
%Trending Utility

global Exp
global userPars

%try
kfiltLim=userPars.kfiltLim;
%catch
%kfiltLim=str2double(userPars.BPdefault(6));
%end

if get(handles.CompositeTog1, 'Value')
  cmpTogFlg=1;
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
  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
          
          % 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));
          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));
          else
            LsmpMax=max(Exp(expN).Trace(trc).Dexp(DexpN).DM(dm).UsrLvals);
          end
          if LsmpMax> Lmax, Lmax=LsmpMax; end
          bpInd=bpInd+1;
        end
      catch
      end
    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;
          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));  
          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);
            else
              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
          conc2=Exp(expN).Dexp(DexpN).DM.conc2{dm}; 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(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;
        end  %if isequal(get(Exp(1).hOL(trc),'Visible'),'on')
      catch
      end
    end
  end
  %{
    if isequal(tempLB(4:6),'cmp')||isequal(tempLB(3:6),'cmpG'),
        RFcmpFlg=1; 
    else
        RFcmpFlg=0;
    end
  %}
end

% Box Plot Plotting section
if userPars.boxplotFlg==1
  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'}
  % generate data
  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
  width=.5*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);
  else
    ticDim=length(Exp(expN).Dexp(DexpN).DM.drug); 
  end
  for dim=1:ticDim  % LOOP Thru DM perturbations
    shn=0;
    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;
      end
    end
  end
  wid=width * ones(1,length(pos));
    
  % boxplot
  figure
  set(gcf,'OuterPosition',(get(0,'screensize')))
  if strcmpi(BPnotch,'on')
    boxplot(final_res, ...
      'notch', 'on', ...
      'positions', pos,...
      'widths', wid) 
  elseif strcmpi(BPnotch,'off'),
    boxplot(final_res, ...
      'notch', 'off', ...
      'positions', pos,...
      'widths', wid) 
  end
  
  % label, change fontsize
  % y-axis
  set(gca, 'FontSize', fontSize)
  ylim([-.5 (Lmax+10)])
  ylabel('L in Hours', 'FontSize', fontSize)
  
  % x-labels
  text_h=findobj(gca, 'Type', 'text');
  % rotation=45;
  
  for cnt=1:length(text_h)
    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
  squeeze=0.2;
  left=0.02;
  right=1;
  bottom=squeeze;
  top=1-squeeze;
  set(gca, 'OuterPosition', [left bottom right top])
      
  % Remove outliers
  hout=findobj(gca,'tag','Outliers');
  for out_cnt=1 : length(hout)
    if strcmpi(BPoutliers,'on'), 
      set(hout(out_cnt), 'Visible', 'on')
    elseif strcmpi(BPnotch,'off'), 
      set(hout(out_cnt), 'Visible', 'off')
    end
  end
end 

% 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});
catch
  lnwidth=4;
  axisFontSz=36;
  legFontSz=10;
  markerSz=5;
end

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
    range=0;
    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
          tmp=[];
          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)
              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);
            end
            % Make LEGEND list
            % Make Sample Count Label item; 
            if n~=length(Exp(expN).Dexp)
              scnt=strcat(scnt,num2str(cnt),',');
            else
              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};
            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);
            %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; 
          catch
          end
          try
            upperStd(trc,n)=dayMed(trc,n) + dayStd(trc,n);
            lowerStd(trc,n)=dayMed(trc,n) - dayStd(trc,n);
          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)
            hTrendFig=plot(dayNums,dayMed(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=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 
          end
        catch
          hTrendFig=plot(1:n,dayMed(trc,1:n),'lineWidth',2); hold on
          linecolor(trc)={get(hTrendFig,'color')};
          ylabel('Experiment Day Index')
        end
      end
      grid on
      % 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
  
    % 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')
            try
              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
            end
          end
        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,'/','-');
    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
  
  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, '\'));
      else
        lastSlash=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '/'));
      end
      expName=expFolder(lastSlash+1:end);
      if length(expName)>18
        expNm=strcat('-',expName(1:18));
      else
        expNm=strcat('-',expName);
      end
         
      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));
          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);
          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;
          upperStd(trc,n)=dmMed(trc,n) + dmStd(trc,n);
          lowerStd(trc,n)=dmMed(trc,n) - dmStd(trc,n);
        end  
      end
       
      % 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')
            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 
      end
      grid on 
      % set(gca,'linewidth',4) %0.5  then 1.5  now 6
      % set(gca,'fontsize',axisFontSz)  % 8  to 15 to 21 
      hold all
    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)  
      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
    end

    mm=1;  
    for nn=1:length(NmLst)
      if iscellstr(NmLst(nn))
        legName(mm)=strrep(NmLst(nn),'_','-');
        mm=mm+1;
      end
    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
  hold off   
end  %if userPars.boxplotFlg~=1   %PLOT OVERLAY OF TRENDS 266