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

% EZplotUcmp.m
% User find and build composite of Selected Gene Composite and
% Plot it on OLay Plot and Trend plot DNLaxles
% For Single and Multi experiment Studies 
% Called when Composite_ toggle button is clicked.
% Data stored for printable Trend Plot production (click [L] in DNLaxes )

global ghandles
global Exp
global exDlst

traceN=Exp(expN).traceN;
DexpN=Exp(expN).DexpN;
dmSel=Exp(zoneSel).Dexp(DexpN).pertSel;
% dmSel=str2num(get(ghandles.DMed3,'string'))
patrnN=strfind(selGnOrf{1},':'); % extract Gene-Orf Name
patrndash=strfind(selGnOrf{1},'-');
selStrNm=char(selGnOrf);
usrGene=selStrNm(1:(patrnN(1)-1));

if strcmpi(selStrNm(1:3),'RF-')
  usrGeneSearch=selStrNm(4:(patrndash(2)-1));    
elseif strcmp(selStrNm(1:3),'RF1')
  usrGeneSearch=selStrNm(1:3);
else
  usrGeneSearch=selStrNm(1:(patrnN(1)-1));
end

prompt={'Enter Specifics Term if used to futher specify selection '};       
dlg_title='User Specifics Term for Refinement Composite';
num_lines=1;
def={'None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
usrSpec=cell2mat(answer(1));

if strcmpi(usrSpec,'None'), usrGnSp={strcat(usrGene,'-')}; 
elseif length(usrSpec)> 8, 
  trimUspec=usrSpec(1:8); 
  usrGnSp=strcat(usrGene,',',{trimUspec});   
else
  trimUspec=usrSpec;
  usrGnSp=strcat(usrGene,',',{trimUspec}); 
end
         
% For n=DexpN:DexpN  %n=1:Exp(expN).DexpLength   %LOOP Thru DayExps
n=DexpN;
MPnum=length(Exp(expN).Dexp(DexpN).MP);
DMnum=length(Exp(expN).Dexp(DexpN).DM.drug);
% Extract expDay from ExpName string
dayNpos=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
dayLbl=Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
dRF1indx=0;
usrSp=usrSpec;  % user entry of Specifics for Ref selection

for mp=1:length(Exp(expN).Dexp(DexpN).MP) 
  for ind384=1:384   
    try      
      % Insert test for numeric in genename and orf if isnumeric
      % Correct common EXCEL problem of converting OCT1 into a date numeric
      if cell2mat(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384))==38991,
          Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)={'OCT1_'}; 
      elseif isnumeric(cell2mat(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)))
          Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)={' '}; 
      end
              
      % DISPersed REFerence capture and find Medians                
      if ( ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
      strcmpi((Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384)),usrSp))) || ...
      ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
      strcmpi(usrSp,'None'))) ),
        dRF1indx=dRF1indx+1;
        Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),':',' ');
        drf(dRF1indx,1)=(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384));
        drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)=mp;
        drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)=ind384;
        %drf(dRF1indx,7)=(Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384));  
      end      
    catch
      msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
    end   
  end
  mp 
end

vvL=[];  % initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
if exist('drf','var')
  % Det. index of change from one MP to the next    
  i=2;
  clear chgIndx
  chgIndx(1)=1;
  for j=1:length(drf(:,3))
    if j>1
      if cell2mat(drf(j,2))~=cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end
    end
  end
  chgIndx(length(chgIndx)+1)=size(drf,1) +1; % length(drf)+1;  
  vvL=zeros(size(drf,1),1 ); % length(drf)+1;
  dMPs=unique(cell2mat(drf(:,2))); 
  for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)
    for mm=1:length(dMPs) % length(chgIndx)
      usrScNdisp=((dMPs(mm)-1)*DMnum)+(d); 
      NZusrIndx=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); 
      medianIndxDisp=NZusrIndx;
      vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5);
      vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
      vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4);
    end

    % CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES
    % for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)
    NZusrIndxG=[];
    NZusrIndxG=find(vvL);   
 
    if isempty(nonzeros(vvL))
      nonZeroCntD=0;  
    else 
      nonZeroCntD=length(nonzeros(vvL)); 
    end
    %Calc. of median value for composite doesn't require and odd number of Indx items
    NZusrIndxG=NZusrIndxG(:);
    if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero 
      UsrLvals{d}=vvL(NZusrIndxG);
      UsrKvals{d}=vvK(NZusrIndxG);
      Usrrvals{d}=vvr(NZusrIndxG);
    end
  end 
end

if ~exist('drf','var')
  errordlg('Gene-Specifics combination not found. Check spelling of Specifics entry.','Entry Warning');
  break; 
end

NoGrowthflg=0;
if isempty(vvL)
  warndlg('No Growth condition found for Gene-Specifics combination. . ','No Growth warning');
  NoGrowthflg=1;
end

% Plot Values Selected Gene-Specifics Composite
if NoGrowthflg==0
  smpSz=size(NZusrIndxG,1);
  K=median(cell2mat((UsrKvals(dmSel)))); Ks=num2str(K);  Kstd=std(cell2mat((UsrKvals(dmSel)))); KstdStr=num2str(Kstd);
  r=median(cell2mat((Usrrvals(dmSel)))); rs=num2str(r);  rstd=std(cell2mat((Usrrvals(dmSel)))); rstdStr=num2str(rstd);
  l=median(cell2mat((UsrLvals(dmSel)))); Ls=num2str(l);  Lstd=std(cell2mat((UsrLvals(dmSel))));  LstdStr=num2str(Lstd);
  Kl=K - Kstd;  %std(UsrKvals(dmSel));  
  Ku=K + Kstd;  %std(UsrKvals(dmSel));  
  rl=r - rstd;  %std(Usrrvals(dmSel));  
  ru=r + rstd;  %std(UsrKvals(dmSel));  
  lfast=l - Lstd;
  lslow=l + Lstd;
elseif NoGrowth==1 % if all data is zero (NoGrowth)
  smpSz=size(NZusrIndxG,1);
  K=0; Ks=num2str(K); Kstd=0; KstdStr=num2str(0);
  r=0; rs=num2str(r); rstd=0; rstdStr=num2str(0);
  l=0; Ls=num2str(l); Lstd=0; LstdStr=num2str(0);
  Kl=K - Kstd;  
  Ku=K + Kstd;  
  rl=r - rstd;  
  ru=r + rstd;  
  lfast=l - Lstd;
  lslow=l + Lstd;
end
    
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
        
plateNum=(LBmp-1)*destPerMP + dmSel;
MP=Exp(zoneSel).Dexp(DexpN).MP;
           
try
  t=1:200;
  clear g;
  try
    g=K ./ (1 +  exp(-r.* (t - l )));
    gSlow=Kl ./ (1 +  exp(-rl.* (t - lslow )));
    gFast=Ku ./ (1 +  exp(-ru.* (t - lfast )));
    if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
    if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
      Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
      Exp(1).traceN=Exp(1).traceN+1;
      traceN=Exp(1).traceN;
    end
    if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
      Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
      Exp(2).traceN=Exp(2).traceN+1;
      traceN=Exp(2).traceN;
    end
    if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
      Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
      Exp(3).traceN=Exp(3).traceN+1;
      traceN=Exp(3).traceN;
    end
    plot(plotAxes,t,g);hold (plotAxes,'on');
    plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
    Exp(expN).Trace(traceN).UsrGLB=usrGnSp;
    Exp(expN).Trace(traceN).dmSel=dmSel;
    Exp(expN).Trace(traceN).DexpN=DexpN;
    for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)  %LOOP Thru DrugMedias 
      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrLvals=UsrLvals(d);
      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrKvals=UsrKvals(d);
      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).Usrrvals=Usrrvals(d);
    end

    % Store L R and K valves for manual selected Composite [C] plots
    Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
    Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;                       

    try 
      for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end
    catch
    end

    Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
    set(Exp(zoneSel).hOL(traceN),'color',[1 0 0]) 
  catch  
    catchissue='Ln100 EZlstBoxExt'
  end

  % Get the DM agar description
  if expN==1,DMstr=char(get(handles.DM1,'string'));end
  if expN==2,DMstr=char(get(handles.DM2,'string'));end
  if expN==3,DMstr=char(get(handles.DM3,'string'));end
  gene=usrGnSp; orf=''   %MP(1,LBmp).orf{1,1}(indx);
  geneOrfstr=strcat(gene,'_',orf,'_');
  grfgenestr=strcat(gene,'_',orf,'_');
  graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
  spotDescrip=strcat(graphStr,'->',DMstr);

  xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
  if ispc,
    slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
  else
    slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
  end
    
  startPos=slashPos(length(slashPos)-1) +1;
  endPos=slashPos(length(slashPos)) -1
  expStr={xp(startPos:endPos)}

  Exp(zoneSel).hOLname(traceN)=spotDescrip;  
  Exp(zoneSel).hOLexpNm(traceN)=expStr;  
  Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
  Exp(zoneSel).hOLplateNum(traceN)=plateNum; 

  if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end  % Displays the value.
  if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
  if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
  if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end  %graphStr);end % Displays the value.
  if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end  %graphStr);end    
  if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end  %graphStr);end
catch
  catchissue='Ln141 EZlstBoxExt'
  msg='Error'
end