%single gene L based interaction shift display
%function EZinteractDev5

global Exp

DexpLen= Exp(expN).DexpLength;
       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;
       if expN==1,pertSel=floor(get(handles.DMsldr1,'value')); end
       if expN==2,pertSel=floor(get(handles.DMsldr2,'value')); end
       if expN==3,pertSel=floor(get(handles.DMsldr3,'value')); end
if sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmean'))&&...
        ~isempty(Exp(expN).Dexp(DexpN).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmeanG'))&&...
        isempty(Exp(expN).Dexp(DexpN).RFmeanG)
    RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmean'))==0 ||...
        isempty(Exp(expN).Dexp(DexpN).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmeanG'))&&...
        ~isempty(Exp(expN).Dexp(DexpN).RFmeanG)
    RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmean'))&&...
        ~isempty(Exp(expN).Dexp(DexpN).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmeanG'))&&...
        ~isempty(Exp(expN).Dexp(DexpN).RFmeanG)
    RFconfig=3;
end
if (sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmean'))==0 ||...
        isempty(Exp(expN).Dexp(DexpN).RFmean))&&...
    (sum(ismember(fieldnames(Exp(expN).Dexp(DexpN)),'RFmeanG'))==0||...
        isempty(Exp(expN).Dexp(DexpN).RFmeanG))
    return
end

%RFconfig= 2;  %1= FullPlateOnly; 2= DistributedOnly; 3= Both FullPlate && Distributed

if RFconfig==1, 
defaultanswer={'80','60','100','3,4,5','N','39','Y'};
end

if RFconfig==2, 
    QctrlRF= 'Select Distributed Control RF option: (G)Global, (L)Local';
    QpertRF= 'Select Distributed Perturbation RF option: (G)Global, (L)Local'; 
   defaultanswer={'80','60','100','3,4,5','N','39','Y','G','L'};
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={'80','60','100','3,4,5','N','39','Y','F','L'};

end 


 %User Input decode for application  ***************************
 if RFconfig==1,
 prompt={'Enter LeftSide Central Boundary in Percent:',...
        'Enter RightSide Central Boundary in Percent:', ...
        'Enter percent of Reference Standard Deviation to use', ...
        'Enter Day Sequence Numbers for set intersect:' ...
        'Remove No Growth Infinite Interactors:' ...
        'Number of Bins for Histograms'...
        'Subplots(Y), Multiple Plots(N), Suspend Plots(S)'};
 else
       prompt={'Enter LeftSide Central Boundary in Percent:',...
        'Enter RightSide Central Boundary in Percent:', ...
        'Enter percent of Reference Standard Deviation to use', ...
        'Enter Day Sequence Numbers for set intersect:' ...
        'Remove No Growth Infinite Interactors:' ...
        'Number of Bins for Histograms'...
        'Subplots(Y), Multiple Plots(N), Suspend Plots(S)',...
        QctrlRF,...
        QpertRF,...
        };
 end       
name='Interaction User Input';
numlines=1;
%defaultanswer={'80','60','100','3,4,5','N','39','Y','0,',''};
answer=inputdlg(prompt,name,numlines,defaultanswer);

negPercent= str2double(cell2mat(answer(1)));
posPercent= str2double(cell2mat(answer(2)));
percentRs=  str2double(cell2mat(answer(3)));
DMstr= cell2mat(answer(4));
   DMcomas=strfind((cell2mat(answer(4))),',');
removInfinL= answer(5);
numBins= str2double(cell2mat(answer(6)));
subplotX= answer(7);
   
n=0;
for i= DMcomas,
    n=n+1
    DMsel(n)= str2double(DMstr(i-1:i))
    if i== max(DMcomas)
        DMsel(n+1)= str2double(DMstr(i:end));
    end       
end
  if strcmp(Exp(expN).DexpType,'chrono'), daysSel= DMsel; end
%**************************************************************
dmN= length(Exp(expN).Dexp(DexpN).DM.drug);
mpN= length(Exp(expN).Dexp(DexpN).MP);
%Intc1=3; IntcLst=5;
%Calculate Interaction values (with and without
%standardDeviation/Upper-Lower boundary compensation

%{
if strcmp(Exp(expN).DexpType, 'single') || strcmp(Exp(expN).DexpType, 'multi')
    DMs2use= DMsel;
    Dexps2use= DexpN;
elseif strcmp(Exp(expN).DexpType, 'chrono')
    DMs2use= pertSel;
    nn= daysSel;
end
%}  

for j= 1:1:DexpLen  
    %nn= daysSel(j);
  for m=1:mpN 
      scnN= pertSel + (dmN*(m-1))
      %****************
      DM0= pertSel;  %the DrugMedia choice is constant based on left screeen choice
      DMj= pertSel;  %j here is the Day experiment number Which 
      DexpN= j; %Day experiment is also where to find data%nn;
      anN= [8 9];
      %****************
      EZintRFs       %* Call subroutine to interpret user RF inputs
      %****************
      DexpN= Exp(expN).DexpN;  %reestablish DexpN 
      %****************
    Xn{m,j,:}=Exp(expN).Dexp(j).scan(scnN).plate(1).CFout(:,5);  %Exp(expN).Dexp(nn).scan(DM{j}(m)).plate(1).CFout(:,5);
    Xn{m,j,:}(Xn{m,j,:}==0)= 140;
    Xln{m,j,:}=Exp(expN).Dexp(j).scan(scnN).plate(1).CFout(:,11);  %Exp(expN).Dexp(nn).scan(DM{j}(m)).plate(1).CFout(:,11);
    Xhn{m,j,:}=Exp(expN).Dexp(j).scan(scnN).plate(1).CFout(:,12);  %Exp(expN).Dexp(nn).scan(DM{j}(m)).plate(1).CFout(:,12);

   %methCalc=1;
   intL{m,j,:} =  ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
   intL{m,j,:}(Xn{m,j,:}==140)= 100;
   intL{m,j,:}(intL{m,j,:}==0)=-0.1;

 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)=0.2; end
     if deltaRn(j)==0, deltaRn(j)=0.2; 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
    
  %**************************************************************************   
   %end %if methCalc==0
   
   deltaXR{m,j,:}(Xn{m,j,:}==140)= 100;
   deltaXR{m,j,:}(Xln{m,j,:}==0)= 100;
   deltaXR{m,j,:}(isnan(Xln{m,j,:}))= 120;
   deltaXR{m,j,:}(Xhn{m,j,:}==0)= 100;
   deltaXR{m,j,:}(isnan(Xhn{m,j,:}))= 120;
  
           
   
   
   %Compile all gene related L values for the each Dexp sequencially(j).
   addend= (1+((m-1)*384))  %((((m-1)*j)*384)+1);
   intLcmp(addend:addend+383,j)= cell2mat(intL(m,j,:));  %For only pertSel across Dexps (((addend:addend+383),j)= cell2mat(intL(j,m,:));
   intLadjcmp(addend:addend+383,j)= cell2mat(deltaXR(m,j,:));  %((addend:addend+383),j)= cell2mat(deltaXR(j,m,:));
  
  end   %m=1:mpN
  %********END m loop assoc'd with MPs for loop***************
  %***********************************************************
  
  
  %Remove RFs and Blank (or non annotated ' ') orf data Then
  %Filter data per user intput
  intLc{j}= intLcmp(:,j);   %j);
  intLwoRFs{j}(1,:)= intLcmp(Exp(expN).Dexp(j).mutSpotIndx.woRFs,j);
  intLwoRFs{j}(2,:)= Exp(expN).Dexp(j).mutSpotIndx.woRFs;%Index of non-RF non-blank spots 
  
  if strcmpi(removInfinL,'Y')     
      
     intLwoRFs0{j}(1,:)= intLwoRFs{j}(1,(intLwoRFs{j}(1,:)~= 100));   %Values intLcmp(Exp(1).mutSpotIndx.woRFs,j);
     intLwoRFs0{j}(2,:)= intLwoRFs{j}(2,(intLwoRFs{j}(1,:)~= 100));   %MP Spot Index position   intLcmp(385:(mpN-1)*384,j);
     clear intLwoRFs
     intLwoRFs{j}(1,:)= intLwoRFs0{j}(1,:);
     intLwoRFs{j}(2,:)= intLwoRFs0{j}(2,:);  
  end
  
  
  intLwoRFsorted{j}= sortrows(intLwoRFs{j}',1); %SortBy Values field
  
  clear intLcmpSortGT0 intLcmpSortLT0
  tempIntL= intLwoRFsorted{j}(:,1);
  intLcmpSortGT0= tempIntL((tempIntL) >0);
  if ~isempty(intLcmpSortGT0)
    centPosCnt= round(posPercent/100 * length(intLcmpSortGT0));
    intLposSel{j}=intLwoRFsorted{j}((length(intLcmpSortGT0)+centPosCnt): end,:);
    posIntboundryCentralVal(j)= intLcmpSortGT0((centPosCnt),:);   %For Histogram use
  else
      posIntboundryCentralVal(j)= 0;
  end
   
  intLcmpSortLT0=  tempIntL((tempIntL) <0);
  if ~isempty(intLcmpSortLT0)
    centNegCnt= round(negPercent/100 * length(intLcmpSortLT0));
    intLnegSel{j}=intLwoRFsorted{j}((1:(length(intLcmpSortLT0)-centNegCnt)),:);
    negIntboundryCentralVal(j)= intLcmpSortLT0(((length(intLcmpSortLT0))-(centNegCnt)),:);  %For Histogram use
  else
      negIntboundryCentralVal(j)=0;
  end
  
    
 %Find potential Interactors within selected range 
  jj=j;
  daysSel= daysSel;
  %maxNperts= Exp(expN).DexpLength; %(daysSel);  %(daysSel);
  
  if jj== daysSel(1)    %Intc1,
        InterslstPos{1}= intLposSel{daysSel(1)}(:,2)   %intLcmpposInd{Intc1}
        InterslstNeg{1}= intLnegSel{daysSel(1)}(:,2)   %intLcmpnegInd{Intc1}
   elseif sum(ismember(daysSel,jj))==1   %Intc1 && jj<=IntcLst
    InterslstPos{1}=(intersect(InterslstPos{1},intLposSel{jj}(:,2)));   %,intLcmpposInd{jj}))
    InterslstNeg{1}=(intersect(InterslstNeg{1},intLnegSel{jj}(:,2)));   %,intLcmpnegInd{jj}))
   end
   
   
  %Convolute experiment spot index to get scan#, MP# and plateIndx needed
  %later to obtain genename and other descriptors and correlate data
 if sum(ismember(daysSel,jj))==1 %might need to? restrict to only the 'daysSel' entered by user
  try
      intLposDIndx{jj}(:,4)= jj;  %Dexp number     
      intLposDIndx{jj}(:,2)= ceil((intLposSel{jj}(:,2))/(384));  %mp plate numb  column
      intLposDIndx{jj}(:,3)=rem(intLposSel{jj}(:,2),(384));   %384));
      tmp= intLposDIndx{jj}(:,3)==0;
      intLposDIndx{jj}(tmp,3)= 384;
      intLposDIndx{jj}(:,1)= pertSel + (dmN*((intLposDIndx{jj}(:,2))-1));   %((intLposDIndx{jj}(:,2))-1));   %scan numb  column  %intLposDIndx(:,2)* intLposDIndx(:,3); 
  catch
  end
  try
      intLnegDIndx{jj}(:,4)= j;  %Dexp number     
      intLnegDIndx{jj}(:,2)= ceil((intLposSel{jj}(:,2))/(384));    %384);  %mp plate numb  column
      intLnegDIndx{jj}(:,3)= rem(intLnegSel{jj}(:,2),(384));
      tmp=(intLnegDIndx{jj}(:,3)==0);
      intLnegDIndx{jj}(tmp,3)= 384;
      intLnegDIndx{jj}(:,1)= pertSel + (dmN*((intLnegDIndx{jj}(:,2))-1));   %scan numb 
  catch
  end
 end    %might want to restrict to only the 'daysSel' entered by user
  %++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  %********************************************************************************************
  %ADJUSTED L for Reference Standard deviation(More conservative) Interaction List compilation
  if strcmpi(removInfinL,'N')     
     intLadjwoRFs{jj}(1,:)=intLadjcmp(Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs,jj);     
     intLadjwoRFs{jj}(2,:)= Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs;        %intLadjcmp(385:(mpN-1)*384,jj); %intLadjcmp(Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs,jj);
    
  elseif strcmpi(removInfinL,'Y')     
     intLadjwoRFs{jj}(1,:)=intLadjcmp(Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs,jj);     
     intLadjwoRFs{jj}(2,:)= Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs;        %intLadjcmp(385:(mpN-1)*384,jj); %intLadjcmp(Exp(expN).Dexp(DexpN).mutSpotIndx.woRFs,jj); 
     intLadjwoRFs100{jj}(1,:)= intLadjwoRFs{jj}(1,(intLadjwoRFs{jj}(1,:)~= 100)) ;   %intLcmp(Exp(1).mutSpotIndx.woRFs,jj);
     intLadjwoRFs100{jj}(2,:)= intLadjwoRFs{jj}(2,(intLadjwoRFs{jj}(1,:)~= 100)) ;   % Remove Index where spots are infinite (=100);
     intLadjwoRFs0{jj}(1,:)= intLadjwoRFs100{jj}(1,(intLadjwoRFs100{jj}(1,:)~= 0));  % Remove Index where spots are indeterminely within the range of Ref STD 
     intLadjwoRFs0{jj}(2,:)= intLadjwoRFs100{jj}(2,(intLadjwoRFs100{jj}(1,:)~= 0));  % Remove Index where spots are indeterminely within the range of Ref STD
     clear intLadjwoRFs
     intLadjwoRFs{jj}(1,:)= intLadjwoRFs0{jj}(1,:); %Put filtered results back into intLadjwoRFs
     intLadjwoRFs{jj}(2,:)= intLadjwoRFs0{jj}(2,:); %Put filtered results back into intLadjwoRFs
  end
 
  intLwoRFsortedAdj{jj}= sortrows(intLadjwoRFs{jj}',1);
  clear intLadjSortGT0 intLadjSortLT0
  tempIntLadj= intLwoRFsortedAdj{jj}(:,1);
  intLadjSortLT0=  tempIntLadj((tempIntLadj) <0);
  intLadjSort0s= tempIntLadj(tempIntLadj ==0)
  intLadjSortGT0= tempIntLadj(tempIntLadj >0);  %=0);
  
  if ~isempty(intLadjSortGT0)&& ~isempty(intLadjSortLT0)
      centPosCntAdj= round(posPercent/100 * length(intLadjSortGT0));
      intLposSelAdj{jj}=intLwoRFsortedAdj{jj}((length(intLadjSortLT0)+ length(intLadjSort0s) + centPosCntAdj): end,:); 
      posIntboundryCentralValAdj(jj)= intLadjSortGT0(centPosCntAdj,:);
  else
      posIntboundryCentralValAdj(jj)= 0;
  end
  
  if ~isempty(intLadjSortLT0) 
     try 
    centNegCntAdj= round(negPercent/100 * length(intLadjSortLT0));
    intLnegSelAdj{jj}=intLwoRFsortedAdj{jj}((1:(length(intLadjSortLT0)-centNegCntAdj)),:);
    negIntboundryCentralValAdj(jj)= intLadjSortLT0(((length(intLadjSortLT0))-(centNegCntAdj)),:);
     catch,negIntboundryCentralValAdj(jj)= 1; 
     end
    else
    negIntboundryCentralValAdj(jj)= 1;
  end

   if jj== daysSel(1)   %Intc1,
        InterslstPosAdj{1}= intLposSelAdj{daysSel(1)}(:,2)   %intLcmpposInd{Intc1}
        InterslstNegAdj{1}= intLnegSelAdj{daysSel(1)}(:,2)   %intLcmpnegInd{Intc1}
   elseif sum(ismember(daysSel,jj))==1   % jj>Intc1 && jj<=IntcLst
    InterslstPosAdj{1}=(intersect(InterslstPosAdj{1},intLposSelAdj{jj}(:,2)));   %,intLcmpposInd{jj}))
    InterslstNegAdj{1}=(intersect(InterslstNegAdj{1},intLnegSelAdj{jj}(:,2)));   %,intLcmpnegInd{jj}))
   end
    
   
  %Convolute experiment spot index to get scan#, MP# and plateIndx needed
  %later to obtain genename and other descriptors and correlate data
  try
      intLposDIndxAdj{jj}(:,2)= ceil((intLposSelAdj{jj}(:,2))/(384));  %mp plate numb  column
      intLposDIndxAdj{jj}(:,4)= jj;
      intLposDIndxAdj{jj}(:,3)=(rem(intLposSelAdj{jj}(:,2),(384)));
      tmp=(intLposDIndxAdj{jj}(:,3)==0);
      intLposDIndx{jj}(tmp,3)= 384;
  intLposDIndxAdj{jj}(:,1)= pertSel + (dmN*((intLposDIndxAdj{jj}(:,2))-1));   %scan numb  column  
  catch
  end
  try
      intLnegDIndxAdj{jj}(:,2)= m;  %ceil((intLnegSelAdj{jj}(:,2))/384);  %mp plate numb  column
      intLnegDIndxAdj{jj}(:,4)= jj;  
      intLnegDIndxAdj{jj}(:,3)=(rem(intLnegSelAdj{jj}(:,2),(384)));
      tmp=(intLnegDIndxAdj{jj}(:,3)==0);
      intLnegDIndxAdj{jj}(tmp,3)= 384;
  intLnegDIndxAdj{jj}(:,1)= pertSel + (dmN*((intLnegDIndxAdj{jj}(:,2))-1));  %scan numb 
  catch
  end
  
%end  %for Perts2use   jj= DMs2use
end  % for j= 1:DexpLen
%****************************************************************************************
%******END OF Big Loop*******************************************************************
%****************************************************************************************




%get interaction values for each DM drugmedia agar type
IntersValsPos= intLcmp(InterslstPos{1},daysSel);
IntersValsNeg= intLcmp(InterslstNeg{1},daysSel);
IntersValsPosAdj= intLadjcmp(InterslstPosAdj{1},daysSel);
IntersValsNegAdj= intLadjcmp(InterslstNegAdj{1},daysSel);
%*********************************************************

%Build 'genelist' data sheet for interactors
if ~isempty(InterslstPos{1})
selIntPx{1}(:,6)=InterslstPos{1};
selIntPx{1}(:,2)=ceil((InterslstPos{1})/(384));  %mp plate numb  column
      selIntPx{1}(:,3)= rem(InterslstPos{1},(384));
      tmpMovV1=(selIntPx{1}(:,3)==0);
      selIntPx{1}(tmpMovV1,3)= 384;
      selIntPx{1}(:,4)= ceil(selIntPx{1}(:,3)/24);  %row numb
      selIntPx{1}(:,5)= rem(selIntPx{1}(:,3),24);
      tmp2=(selIntPx{1}(:,5)==0);
      selIntPx{1}(tmp2,5)= 24;
  selIntPx{1}(:,1)= pertSel + (dmN*((selIntPx{1}(:,2))-1));   %scan numb  column  %intLposDIndx(:,2)* intLposDIndx(:,3); 
  selIntP= cell2mat(selIntPx);
end
if ~isempty(InterslstNeg{1})
  selIntNx{1}(:,6)=InterslstNeg{1};
  selIntNx{1}(:,2)=ceil((InterslstNeg{1})/(384));  %mp plate numb  column
      selIntNx{1}(:,3)=(rem(InterslstNeg{1},(384)));
      tmp1=(selIntNx{1}(:,3)==0);
      selIntNx{1}(tmp1,3)= 384;
      selIntNx{1}(:,4)= ceil(selIntNx{1}(:,3)/24);  %row numb
      selIntNx{1}(:,5)= rem(selIntNx{1}(:,3),24);
      tmp2=(selIntNx{1}(:,5)==0);
      selIntNx{1}(tmp2,5)= 24;

  selIntNx{1}(:,1)= pertSel + (dmN*((selIntNx{1}(:,2))-1));  %jj + (maxNperts*((selIntNx{1}(:,2))-1));   %scan numb
  selIntN= cell2mat(selIntNx);
end

if strcmp(Exp(expN).DexpType, 'single') || strcmp(Exp(expN).DexpType,'multi')
    d1= DexpN;
elseif strcmp(Exp(expN).DexpType, 'chrono')
    d1= daysSel(1);  %Dexps2use(1);
end
if ~isempty(InterslstPos{1})
for i=1:size(selIntP,1)
  IPgene(i)=Exp(expN).Dexp(d1).MP(selIntP(i,2)).genename{1}(selIntP(i,3));
  IPorf(i)= Exp(expN).Dexp(d1).MP(selIntP(i,2)).orf{1}(selIntP(i,3));
  IPstrain(i)= Exp(expN).Dexp(d1).MP(selIntP(i,2)).strain{1}(selIntP(i,3));
  IPspecifics(i)=Exp(expN).Dexp(d1).MP(selIntP(i,2)).specifics{1}(selIntP(i,3));
  IPorfRep(i)=Exp(expN).Dexp(d1).MP(selIntP(i,2)).orfRep{1}(selIntP(i,3));  
  
  %Bad this is the L data for only the last selected DM perturbation
  %Would need to calculate each scan# for each perts2use value
  ipL(i)= Exp(expN).Dexp(d1).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),5);
  ipLlower(i)= Exp(expN).Dexp(d1).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),11);
  ipLupper(i)= Exp(expN).Dexp(d1).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),12);
  %*************************************************************************
end
end
if ~isempty(InterslstNeg{1})
for i=1:size(selIntN,1)
    i
  INgene(i)=Exp(expN).Dexp(d1).MP(selIntN(i,2)).genename{1}(selIntN(i,3));
  INorf(i)= Exp(expN).Dexp(d1).MP(selIntN(i,2)).orf{1}(selIntN(i,3));
  INstrain(i)= Exp(expN).Dexp(d1).MP(selIntN(i,2)).strain{1}(selIntN(i,3));
  INspecifics(i)=Exp(expN).Dexp(d1).MP(selIntN(i,2)).specifics{1}(selIntN(i,3));
  INorfRep(i)=Exp(expN).Dexp(d1).MP(selIntN(i,2)).orfRep{1}(selIntN(i,3));    
  
  %Bad this is the L data for only the last selected DM perturbation
  %Would need to calculate each scan# for each perts2use value
  inL(i)= Exp(expN).Dexp(d1).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),5);
  inLlower(i)= Exp(expN).Dexp(d1).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),11);
  inLupper(i)= Exp(expN).Dexp(d1).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),12);
  %*************************************************************************
end
end
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%**************************************************************************************
%ADJUSTED with STD and curve fit boundaries to produce more conservative interaction values 

%Build 'genelist' data sheet for interactors
selIntPxAdj{1}(:,2)=ceil((InterslstPosAdj{1})/(384));  %mp plate numb  column
      selIntPxAdj{1}(:,3)=(rem(InterslstPosAdj{1},(384)));
      tmpMovV1=(selIntPxAdj{1}(:,3)==0);
      selIntPxAdj{1}(tmpMovV1,3)= 384;
      selIntPxAdj{1}(:,4)= ceil(selIntPxAdj{1}(:,3)/24);  %row numb
      selIntPxAdj{1}(:,5)= rem(selIntPxAdj{1}(:,3),24);
      tmpMovV2=(selIntPxAdj{1}(:,5)==0);
      selIntPxAdj{1}(tmpMovV2,5)= 24;
      
  selIntPxAdj{1}(:,1)= pertSel + (dmN*((selIntPxAdj{1}(:,2))-1));  %scan numb  column  %intLposDIndx(:,2)* intLposDIndx(:,3); 
  selIntPAdj= cell2mat(selIntPxAdj);
 
if ~isempty(InterslstNegAdj{1})
  selIntNxAdj{1}(:,2)=ceil((InterslstNegAdj{1})/(384));  %mp plate numb  column
      selIntNxAdj{1}(:,3)= rem(InterslstNegAdj{1},(384));
      tmpMovV1=(selIntNxAdj{1}(:,3)==0);
      selIntNxAdj{1}(tmpMovV1,3)= 384;
      selIntNxAdj{1}(:,4)= ceil(selIntNxAdj{1}(:,3)/24);  %row numb
      selIntNxAdj{1}(:,5)= rem(selIntNxAdj{1}(:,3),24);
      tmpMovV2=(selIntNxAdj{1}(:,5)==0);
      selIntNxAdj{1}(tmpMovV2,5)= 24;

  selIntNxAdj{1}(:,1)= pertSel + (dmN*((selIntNxAdj{1}(:,2))-1));  %scan numb
  selIntNAdj= cell2mat(selIntNxAdj);
end
for i=1:size(selIntPAdj,1)
  IPgeneAdj(i)=Exp(expN).Dexp(d1).MP(selIntPAdj(i,2)).genename{1}(selIntPAdj(i,3));
  IPorfAdj(i)= Exp(expN).Dexp(d1).MP(selIntPAdj(i,2)).orf{1}(selIntPAdj(i,3));
  IPstrainAdj(i)= Exp(expN).Dexp(d1).MP(selIntPAdj(i,2)).strain{1}(selIntPAdj(i,3));
  IPspecificsAdj(i)=Exp(expN).Dexp(d1).MP(selIntPAdj(i,2)).specifics{1}(selIntPAdj(i,3));
  IPorfRepAdj(i)=Exp(expN).Dexp(d1).MP(selIntPAdj(i,2)).orfRep{1}(selIntPAdj(i,3));  
  
  %Bad this is the L data for only the last selected DM perturbation
  %Would need to calculate each scan# for each perts2use value
  ipLAdj(i)= Exp(expN).Dexp(d1).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),5);
  ipLlowerAdj(i)= Exp(expN).Dexp(d1).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),11);
  ipLupperAdj(i)= Exp(expN).Dexp(d1).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),12);
  %************************************************************************************
end
if ~isempty(InterslstNegAdj{1})
for i=1:size(selIntNAdj,1)
  INgeneAdj(i)=Exp(expN).Dexp(d1).MP(selIntNAdj(i,2)).genename{1}(selIntNAdj(i,3));
  INorfAdj(i)= Exp(expN).Dexp(d1).MP(selIntNAdj(i,2)).orf{1}(selIntNAdj(i,3));
  INstrainAdj(i)= Exp(expN).Dexp(d1).MP(selIntNAdj(i,2)).strain{1}(selIntNAdj(i,3));
  INspecificsAdj(i)=Exp(expN).Dexp(d1).MP(selIntNAdj(i,2)).specifics{1}(selIntNAdj(i,3));
  INorfRepAdj(i)=Exp(expN).Dexp(d1).MP(selIntNAdj(i,2)).orfRep{1}(selIntNAdj(i,3));    
  
  %Bad this is the L data for only the last selected DM perturbation
  %Would need to calculate each scan# for each perts2use value
  inLAdj(i)= Exp(expN).Dexp(d1).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),5);
  inLlowerAdj(i)= Exp(expN).Dexp(d1).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),11);
  inLupperAdj(i)= Exp(expN).Dexp(d1).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),12);
  %*************************************************************************************
end
end
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

%Plot Histogram******************************************************

%subplotX=1;
figure
RFstds=', ';
for jj=1:DexpLen, 
    RFstds=strcat(RFstds,'Rs',num2str(jj),'_',num2str(Rs(jj)));
if jj~=DexpLen, strcat(RFstds,', ');end
end              
histName= strcat('ExpZone ',num2str(expN),'-',Exp(expN).Dexp(DexpN).ExpFoldr,', Interaction Values ',  ...
       ', LfFilter-',num2str(negPercent),', RtFilter-',num2str(posPercent),', RemoveNoGrowth-',char(removInfinL), ...
       RFstds)
histAdjName= strcat('ExpZone ',num2str(expN),'-',Exp(expN).Dexp(DexpN).ExpFoldr,', Interaction Compensated by Reference Standard Deviation @',num2str(percentRs),'%', '& Upper/Lower Curvefit Boundaries', ...
       ', LfFilter-',num2str(negPercent),', RtFilter-',num2str(posPercent),', RemoveNoGrowth-',char(removInfinL), ...
       RFstds)
 if strcmpi(subplotX,'Y')
    for jj=1:DexpLen
        histLdata= intLwoRFsorted{jj}(:,1);       %intLcmp(385:(mpN-1)*384,jj);
        %histLadjData= intLadjcmp(385:(mpN-1)*384,jj);
        hgLdat{jj}=histfitJR(histLdata,numBins,'kernel');
        
       x{jj}= get(hgLdat{jj}(2),'xdata');
       y{jj}= get(hgLdat{jj}(2),'ydata');
       xb{jj}=get(hgLdat{jj}(1),'xdata');
       yb{jj}=get(hgLdat{jj}(1),'ydata');
       ybpostot{jj}=sum(yb{jj}(2,(xb{jj}(1,:)>=0)));
       ybnegtot{jj}=sum(yb{jj}(2,(xb{jj}(1,:) <0)));
       xbb(jj,:)=xb{jj}(2,:);
       ybb(jj,:)=yb{jj}(2,:);
       clf
    end
   
   % figure
   
   
   if strcmpi(removInfinL,'N') 
       histLadjData= intLwoRFsortedAdj{jj}(:,1);  %intLadjcmp(385:(mpN-1)*384,jj);
      else
       intLwoRFsortedAdj4HisW0{jj}= sortrows(intLadjwoRFs100{jj}',1);  %Data including with 0's indeterminate within STD
       histLadjData= intLwoRFsortedAdj4HisW0{jj}(:,1)
   end
   for jj=1:DexpLen
     histLdata= intLwoRFsorted{jj}(:,1);        %intLcmp(385:(mpN-1)*384,jj);    
       hgL{jj}=subplot(2, 4, jj), histfitJR(histLdata,numBins,'kernel') ; hold  %hgL{jj}=histfit(intLcmp(:,jj),31,'kernel')
       subplot(2, 4, jj),plot(posIntboundryCentralVal(jj), 1:3000,'--r')
       subplot(2, 4, jj),plot(negIntboundryCentralVal(jj), 1:3000,'--g')
       hold off
   end
   scnsize=get(0,'screensize')
   pos1= [round(scnsize(3)/40), round(scnsize(4)/2 +(scnsize(3)/80)),...
       round(scnsize(3) -round(scnsize(3)/80)),round(scnsize(4)/2 -round(scnsize(4)/80))]
   set(gcf,'outerposition',pos1)
   set(gcf,'Name', histName);
   
   figure
   

   for jj=1:DexpLen
      if strcmpi(removInfinL,'N') 
       histLadjData= intLwoRFsortedAdj{jj}(:,1);  %intLadjcmp(385:(mpN-1)*384,jj);
      else
       intLwoRFsortedAdj4HisW0{jj}= sortrows(intLadjwoRFs100{jj}',1);  %Data including with 0's indeterminate within STD
       histLadjData= intLwoRFsortedAdj4HisW0{jj}(:,1)
      end
       hgLadj{jj}=subplot(2, 4, jj),histfitJR(histLadjData,numBins,'kernel') ; hold   %hgLadj{jj}=histfit(intLadjcmp(:,jj),31,'kernel')
       subplot(2, 4, jj),plot(posIntboundryCentralValAdj(jj), 1:3000,'--r')
       subplot(2, 4, jj),plot(negIntboundryCentralValAdj(jj), 1:3000,'--g')
       hold off
   end
   pos2= [round(scnsize(3)/40), round(scnsize(4)/30),...
       round(scnsize(3) -scnsize(3)/80),round(scnsize(4)/2 -scnsize(4)/80)]
   set(gcf,'outerposition',pos2)
   set(gcf,'Name', histAdjName)
   %set(gcf,'Name', 'Interaction Compensated by Standard Deviation and Upper/Lower Curvefit boundaries')
   
elseif strcmpi(subplotX,'N')    
for jj=1:DexpLen
   
   histLdata= intLwoRFsorted{jj}(:,1);     %intLcmp(385:(mpN-1)*384,jj);
       %intLwoRFsortedAdj4HisW0{jj}= sortrows(intLadjwoRFs100{jj}',1);  %Data including with 0's indeterminate within STD
       %histLadjData= intLwoRFsortedAdj4HisW0{jj}(:,1);
      %histLadjData= intLwoRFsortedAdj{jj}(:,1);  %intLadjcmp(385:(mpN-1)*384,jj);%intLadjcmp(385:(mpN-1)*384,jj);  %intLcmp(:,jj);  %intLadjcmp(:,jj);
   if strcmpi(removInfinL,'N') 
       histLadjData= intLwoRFsortedAdj{jj}(:,1);  %intLadjcmp(385:(mpN-1)*384,jj);
    else
     intLwoRFsortedAdj4HisW0{jj}= sortrows(intLadjwoRFs100{jj}',1);  %Data including with 0's indeterminate within STD
     histLadjData= intLwoRFsortedAdj4HisW0{jj}(:,1)
   end 
figure    
hgL{jj}=histfitJR(histLdata,numBins,'kernel') ; hold  %hgL{jj}=histfit(intLcmp(:,jj),31,'kernel')
plot(posIntboundryCentralVal(jj), 1:3000,'--r')
plot(negIntboundryCentralVal(jj), 1:3000,'--g')
set(gcf,'Name', strcat('DM-',num2str(jj),'-',histName));
hold off

figure
hgLadj{jj}=histfitJR(histLadjData,numBins,'kernel') ; hold   %hgLadj{jj}=histfit(intLadjcmp(:,jj),31,'kernel')
plot(posIntboundryCentralValAdj(jj), 1:3000,'--r')
plot(negIntboundryCentralValAdj(jj), 1:3000,'--g')
set(gcf,'Name', strcat('DM-',num2str(jj),'-',histAdjName));
hold off

x{jj}= get(hgL{jj}(2),'xdata')
y{jj}= get(hgL{jj}(2),'ydata');
xb{jj}=get(hgL{jj}(1),'xdata')
yb{jj}=get(hgL{jj}(1),'ydata')
ybpostot{jj}=sum(yb{jj}(2,(xb{jj}(1,:)>=0)))
ybnegtot{jj}=sum(yb{jj}(2,(xb{jj}(1,:) <0)))
 
xbb(jj,:)=xb{jj}(2,:);
ybb(jj,:)=yb{jj}(2,:);
end   % for jj=  when subplotX~=1  standard one plot per figure



end   %if subplotX==1    histograms placed in subplot figure  else multiple histogram plots



if strcmpi(subplotX,'Y')
 %{
figure
bar3(ybb);
set(gcf,'Name', 'Unfiltered Interaction Histogram for all DrugMedias; NoGrowth Interactors set to 100hr (highest bin)')
%}
%xxbb=yb{1}(2,:);
%figure
end

EZintPrint
 a=1

 %{   
   if methCalc==0 
   deltaXR{m,j}= zeros(1,384);    
   deltaXR{m,j}(Xn{m,j} >=(Rn(j)+Rs(j)))= ( Xln{m,j}(Xn{m,j} >=(Rn(j)+Rs(j))))- (Rn(j)+Rs(j));
   deltaXR{m,j}(Xn{m,j} < (Rn(j)-Rs(j)))= ( Xhn{m,j}(Xn{m,j} < (Rn(j)-Rs(j))))- (Rn(j)-Rs(j));
   Xneg= Xhn{m,j}- (Rn(j)-Rs(j));
   Xpos= Xln{m,j}- (Rn(j)+Rs(j));
   
   
   for i=1:length(Xpos(:)),
     %deltaXR{m,j}(i)= Xpos(i);
     if deltaXR{m,j}(i)==0
       try
       if abs(Xpos(i))<abs(Xneg(i)), deltaXR{m,j}(i)= Xpos(i);end
       catch, end
     end
   end
   for i=1:length(Xneg(:)),
   if deltaXR{m,j}(i)==0, deltaXR{m,j}(i)= Xneg(i); end
    try    
       if abs(Xpos(i))>abs(Xneg(i)), deltaXR{m,j}(i)= Xneg(i); end
    catch
    end
   end
   %else else else else
   else  %if methCalc~=0
       %percentRs= 100;
       RsReduced(j)= percentRs/100* Rs(j)
       %{
     Yn{m,j}= Xn{m,j}-Xn{m,1};  %Yn is deltaXn
     Yn{m,j}(Yn{m,j}==0)=-0.5;
     Yln{m,j}= Xln{m,j}-Xln{m,1};
     Yln{m,j}(Yln{m,j}==0)=-0.5;
     Yhn{m,j}= Xhn{m,j}-Xhn{m,1};
     Yhn{m,j}(Yhn{m,j}==0)=-0.5;
     %}
       
     %deltaRp(j)= (Rn(j)+RsReduced(j))-Rn(1);  %
     deltaRp(j)= (Rn(j)+RsReduced(j))-(Rn(1)+RsReduced(1));
     %deltaRn(j)= (Rn(j)-RsReduced(j))-Rn(1);  %
     deltaRn(j)=(Rn(j)-RsReduced(j))-(Rn(1)-RsReduced(1));
     if deltaRp(j)==0, deltaRp(j)=0.2; end
     if deltaRn(j)==0, deltaRn(j)=0.2; 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
    
  %**************************************************************************   
   end %if methCalc==0
   %}