750 lines
36 KiB
Mathematica
Executable File
750 lines
36 KiB
Mathematica
Executable File
%EZvInitLoad
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clear Exp
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global Exp
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w=pwd;
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Exp(1).Dexp(1).DexpType='single';
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Exp(2).Dexp(1).DexpType='single';
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Exp(3).Dexp(1).DexpType='single';
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Exp(1).Dexp(1).DexpType= 1;
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Exp(2).Dexp(1).DexpN= 1;
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Exp(3).Dexp(1).DexpN= 1;
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set(handles.GeneOrfTog,'value',0)
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try load 'EZsgdInfo'; catch disp('Fail to load EZsgdInfo file from code directory'); end
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Exp(4).SGDnum=SGDnum;
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Exp(4).SGDtext=SGDtext;
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Exp(4).SGDraw=SGDraw;
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Exp(4).interacPBsel=0;
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try
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%Non PC accommodatition
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if ispc,cd(fullfile('C:\')); % \Easy\Experiments'));
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else
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cd(fullfile('~'))
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end
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[openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
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try
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ExpOutmat= fullfile(openExppath,openExpfile);
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load(ExpOutmat);
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cd(openExppath)
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cd ..;
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resDir=pwd;
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Exp(1).Dexp(1).resDir=resDir;
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Exp(2).Dexp(1).resDir=resDir;
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Exp(3).Dexp(1).resDir=resDir;
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cd ..;
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ExpPath=pwd;
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Exp(1).Dexp(1).ExpFoldr=ExpPath;
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Exp(2).Dexp(1).ExpFoldr=ExpPath;
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Exp(3).Dexp(1).ExpFoldr=ExpPath;
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cd(w)
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load (fullfile(Exp(1).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
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Exp(1).Dexp(1).DM=DM;
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Exp(2).Dexp(1).DM=DM;
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Exp(3).Dexp(1).DM=DM;
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Exp(1).Dexp(1).MP=MP;
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Exp(2).Dexp(1).MP=MP;
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Exp(3).Dexp(1).MP=MP;
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Exp(1).Dexp(1).scan=scan;
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Exp(2).Dexp(1).scan=scan;
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Exp(3).Dexp(1).scan=scan;
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load(fullfile(resDir,'PTmats','NImParameters'))
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Exp(1).Dexp(1).ImParMat=ImParMat;
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Exp(2).Dexp(1).ImParMat=ImParMat;
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Exp(3).Dexp(1).ImParMat=ImParMat;
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try
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load(fullfile(resDir,'Fotos','Coordinates'))
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load(fullfile(resDir,'Fotos','anlZones'))
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load(fullfile(resDir,'Fotos','BGatTpts'))
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Exp(1).Dexp(1).FexpScanSpots=FexpScanSpots;
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Exp(2).Dexp(1).FexpScanSpots=FexpScanSpots;
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Exp(3).Dexp(1).FexpScanSpots=FexpScanSpots;
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Exp(1).Dexp(1).FexpScanBMtp=FexpScanBMtp;
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Exp(2).Dexp(1).FexpScanBMtp=FexpScanBMtp;
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Exp(3).Dexp(1).FexpScanBMtp=FexpScanBMtp;
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Exp(1).Dexp(1).anlZoneRefs=anlZoneRefs;
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Exp(2).Dexp(1).anlZoneRefs=anlZoneRefs;
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Exp(3).Dexp(1).anlZoneRefs=anlZoneRefs;
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catch
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end
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Exp(1).traceN=0; Exp(2).traceN=0; Exp(3).traceN=0; %ZoneRelated
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Exp(1).hOL =[]; Exp(1).hOLb=[];
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Exp(1).hOLname = {}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
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Exp(1).hOLplateNum=[];
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Exp(1).hOLresDir= {};
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Exp(1).RFmd1indx=[];
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Exp(1).RFmd1pltN=[];
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Exp(1).RFmd2indx=[];
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Exp(1).RFmd2pltN=[];
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Exp(2).hOL =[]; Exp(2).hOLb=[];
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Exp(2).hOLname = {}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
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Exp(2).hOLplateNum=[];
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Exp(2).hOLresDir= {};
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Exp(2).RFmd1indx=[];
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Exp(2).RFmd1pltN=[];
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Exp(2).RFmd2indx=[];
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Exp(2).RFmd2pltN=[];
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Exp(3).hOL =[]; Exp(3).hOLb=[];
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Exp(3).hOLname = {}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
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Exp(3).hOLplateNum=[];
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Exp(3).hOLresDir= {};
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Exp(3).RFmd1indx=[];
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Exp(3).RFmd1pltN=[];
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Exp(3).RFmd2indx=[];
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Exp(3).RFmd2pltN=[];
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%sefaults values for EZvFigPrint that meet JLH preferences
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Exp(4).plotPars={'4','36','10','5'};
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expN=1;
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MPnum=length(Exp(expN).Dexp(1).MP);
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set(handles.MPsldr1,'min',1,'max',MPnum)
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set(handles.MPsldr2,'min',1,'max',MPnum)
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set(handles.MPsldr3,'min',1,'max',MPnum)
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DMnum= length(Exp(expN).Dexp(1).DM.drug);
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set(handles.DMsldr1,'min',1,'max',DMnum) %DMnum,'value',1.01) %100,'value',1.01)
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set(handles.DMsldr2,'min',1,'max',DMnum)
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set(handles.DMsldr3,'min',1,'max',DMnum)
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tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
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set(handles.Tptsldr1,'min',1,'max',tPtsSize)
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set(handles.Tptsldr2,'min',1,'max',tPtsSize)
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set(handles.Tptsldr3,'min',1,'max',tPtsSize)
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set(handles.MPsldr1,'SliderStep',[1/length(MP) 1/length(MP)]);
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set(handles.DMsldr1,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
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set(handles.Tptsldr1,'SliderStep',[1/tPtsSize 1/tPtsSize]);
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set(handles.MPsldr2,'SliderStep',[1/length(MP) 1/length(MP)]);
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set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
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set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
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set(handles.MPsldr3,'SliderStep',[1/length(MP) 1/length(MP)]);
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set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
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set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);
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try
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xp=char(Exp(expN).Dexp(1).resDir);
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if ispc,
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slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'\');
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else
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slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'/');
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end
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startPos=slashPos(length(slashPos)-1) +1;
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endPos=slashPos(length(slashPos)) -1;
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expStr= xp(startPos:endPos);
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set(handles.expName1,'string',expStr);
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set(handles.expName2,'string',expStr);
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set(handles.expName3,'string',expStr);
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catch
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cd(w)
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end %internal try xp=char(Exp(expN).Dexp(1).resDir); if ispc,...
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catch
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cd(w)
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msg='LOADing or Setup issue'
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%if no load, then Message try SelExp PB to reload or try and different
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%Experiment
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end %nested try-catch-end from ->ExpOutmat= fullfile(openExppath,openExpfile);
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try
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DNLaxes1= handles.DNLaxes1; DNLaxes2= handles.DNLaxes2; DNLaxes3= handles.DNLaxes3;
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zeroCLn= zeros(1,DMnum);
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Exp(expN).expLoadCnt(1)=1; %ZoneRelated
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Exp(1).hzeroCLn(1) = plot(DNLaxes1,zeroCLn,1:DMnum,'y'); try set(Exp(1).hzeroCLn,'visible','off'); catch ME, end
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Exp(2).hzeroCLn(1) = plot(DNLaxes2,zeroCLn,1:DMnum,'y'); try set(Exp(2).hzeroCLn,'visible','off'); catch ME, end
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Exp(3).hzeroCLn(1) = plot(DNLaxes3,zeroCLn,1:DMnum,'y'); try set(Exp(3).hzeroCLn,'visible','off'); catch ME, end
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Exp(1).expLoadCnt=1;
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Exp(2).expLoadCnt=1;
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Exp(3).expLoadCnt=1;
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catch ME, ME.message,
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end
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%**********************************************************************
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%****Compile GeneList and OrfList,****************************************
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%****Sort and add the medians of Ref Plates if RF1,RF2 exist**************
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set(handles.listboxGnOrf,'string',{('Loading')})
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lstindx=0;
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lstindxOrf=0;
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spN=0;
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rfcnt=0;
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dRF1indx=0;
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RF1mp=[]; RF2mp=[];
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for mp=1:length(Exp(expN).Dexp(1).MP)
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RF1fullPlate=0;
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try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
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RF2fullPlate=0;
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try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
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for ind384=1:384
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spN=spN+1;
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try %temp find data error
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r= ceil(ind384/24);
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if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
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%Insert test for numeric in genename and orf if isnumeric
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%Correct common EXCEL problem of converting OCT1 into a date numeric
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if cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))==38991,
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Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={'OCT1_'};
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%genename{1}(ind384) replace numeric with a space ' ' or something
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elseif isnumeric(cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
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Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={' '};
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end
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%****Check for full(384spot) Reference Plates (RF1 or/and RF2)**************
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RF1fullPlate=0;
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try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
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RF2fullPlate=0;
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try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
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if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))),'blank'))... %,'\<blank\>'
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&& ~isnumeric(Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'')...
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&& ~isempty((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF1')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2')...
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&& iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))) % .genename{1}(ind384)))
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lstindxOrf=lstindxOrf+1;
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bb(lstindxOrf,1)= (Exp(expN).Dexp(1).MP(mp).orf{1}(ind384));
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bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
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bb(lstindxOrf,3)={mp};
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bb(lstindxOrf,4)={r};
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bb(lstindxOrf,5)={c};
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mutorfs(lstindxOrf)=spN; %16_0318 added for Interaction EZinteract
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end
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if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))... %,'\<blank\>'
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&& ~isnumeric(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'')...
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&& ~isempty((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1')...
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&& ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2')...
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&& iscellstr((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
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lstindx=lstindx+1;
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aa(lstindx,1)= (Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
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aa(lstindx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
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aa(lstindx,3)={mp};
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aa(lstindx,4)={r};
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aa(lstindx,5)={c};
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mutgenes(lstindx)=spN;
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%Exp(expN).Dexp(1).mutSpotIndx.woRFs(lstindx)=spN;
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elseif (RF1fullPlate==1 ||... %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384 || ...
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(length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp==1 ) && ... %(isequal((Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(1).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
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~exist('RF1scanN','var')
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RF1mp=mp
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RF1scanN=(mp*DMnum)-(DMnum-1); %mp;
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rfcnt=rfcnt+1;
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RFs(spN:spN+383)= spN:spN+383;
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elseif (RF2fullPlate==1|| ... %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))==384 ||...
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(length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp== length(Exp(expN).Dexp(1).MP) ) && ...
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~exist('RF2scanN','var')
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rfcnt=rfcnt+1;
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RFs(spN:spN+383)= spN:spN+383;
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asdf= sparse(RFs);
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asd=find(asdf);
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RFs=asd;
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RF2mp=mp
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RF2scanN= (mp*DMnum)-(DMnum-1); %mp;
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elseif strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1') && ...
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(RF1fullPlate~=1)
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dRF1indx=dRF1indx+1;
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Exp(expN).Dexp(1).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
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drf(dRF1indx,1)= (Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
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drf(dRF1indx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
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drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)= mp;
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drf(dRF1indx,4)={r}; drfr(dRF1indx,mp)= r;
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drf(dRF1indx,5)={c}; drfc(dRF1indx,mp)= c;
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drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)= ind384;
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end %if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...
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%**********************************************************************
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catch
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error='EZexpSel lineAfter 135 EZvInitLoad.m'
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mp
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ind384
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msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
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end
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end %end associated with for ind384=1:384
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mp
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end %end associated with for mp=1:length(Exp(expN).Dexp(1).MP)
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%*****************************************************
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%Cover case if mutorfs RFs are labeled RF1 or RF2
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try
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Exp(1).Dexp(1).mutSpotIndx.wRFs= union(RFs, mutorfs);
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catch
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msg= 'No RFs Found in Exp! wRFs'
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Exp(1).Dexp(1).mutSpotIndx.wRFs= mutorfs;
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end
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try
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Exp(1).Dexp(1).mutSpotIndx.woRFs= setdiff(mutorfs,RFs);
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catch
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Exp(expN).Dexp(1).mutSpotIndx.woRFs= mutorfs;
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msg= 'No RFs Found in Exp! woRFs'
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end
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Exp(2).Dexp(1).mutSpotIndx.wRFs= Exp(1).Dexp(1).mutSpotIndx.wRFs;
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Exp(2).Dexp(1).mutSpotIndx.woRFs= Exp(1).Dexp(1).mutSpotIndx.woRFs;
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Exp(3).Dexp(1).mutSpotIndx.wRFs= Exp(1).Dexp(1).mutSpotIndx.wRFs;
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Exp(3).Dexp(1).mutSpotIndx.woRFs= Exp(1).Dexp(1).mutSpotIndx.woRFs;
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%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
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Exp(1).Dexp(1).RFmd1indx=[]; Exp(2).Dexp(1).RFmd1indx=[]; Exp(3).Dexp(1).RFmd1indx=[];
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Exp(1).Dexp(1).RFmd1pltN=[]; Exp(2).Dexp(1).RFmd1pltN=[]; Exp(3).Dexp(1).RFmd1pltN=[];
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Exp(1).Dexp(1).RFmean= []; Exp(2).Dexp(1).RFmean= []; Exp(3).Dexp(1).RFmean= [];
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Exp(1).Dexp(1).RFmeanG= []; Exp(2).Dexp(1).RFmeanG= []; Exp(3).Dexp(1).RFmeanG= [];
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if exist('RF1scanN','var')
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for d=0:(DMnum-1)
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medianIndx=[];
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nonZeroIndx=[];
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medValList=[];
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rf1scN=RF1scanN+d;
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try %if RF1scanN doesn't exist this addition to list will be skipped
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nonZeroIndx = find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
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if isempty(nonZeroIndx), nonZeroCnt=0, medianIndx= nonZeroIndx
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else nonZeroCnt=length(nonZeroIndx);
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end
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%
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if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx= nonZeroIndx(1:nonZeroCnt-1); end
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if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx= nonZeroIndx, end
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if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
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medValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5);
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medValList1{d+1}= medValLst;
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min1= min(medValLst);
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max1= max(medValLst);
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std1= std(medValLst);
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mean1= mean(medValLst)
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mval1=median(medValLst); %(Exp(expN).Dexp(1).scan(RF1scanN).plate(1).CFout(383,5));
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RFmd1pos=find(mval1==(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5)))
|
|
RFmd1loc(1)= ceil(RFmd1pos/24); %calc r value
|
|
RFmd1loc(2)= RFmd1pos - ((RFmd1loc(1)-1)*24); %calc c value
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
aa(lstindx,1)= {strcat('RF1md(',num2str(d+1),')')};
|
|
aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,' std',num2str(std1))};
|
|
bb(lstindxOrf,1)= {strcat('RF1md(',num2str(d+1),')')};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,' std',num2str(std1))};
|
|
|
|
Exp(1).Dexp(1).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(1).Dexp(1).RFmd1indx(d+1)=RFmd1pos; Exp(2).Dexp(1).RFmd1indx(d+1)=RFmd1pos; Exp(3).Dexp(1).RFmd1indx(d+1)=RFmd1pos;
|
|
Exp(1).Dexp(1).RFmd1pltN= RF1mp; Exp(2).Dexp(1).RFmd1pltN= RF1mp; Exp(3).Dexp(1).RFmd1pltN= RF1mp;
|
|
Exp(1).Dexp(1).RFmd1val(d+1)= mval1; Exp(2).Dexp(1).RFmd1val(d+1)= mval1; Exp(3).Dexp(1).RFmd1val(d+1)= mval1;
|
|
Exp(1).Dexp(1).mean1(d+1)= mean1; Exp(2).Dexp(1).mean1(d+1)= mean1; Exp(3).Dexp(1).mean1(d+1)= mean1;
|
|
Exp(1).Dexp(1).std1(d+1)= std1; Exp(2).Dexp(1).std1(d+1)= std1; Exp(3).Dexp(1).std1(d+1)= std1;
|
|
Exp(1).Dexp(1).min1(d+1)= min1; Exp(2).Dexp(1).min1(d+1)= min1; Exp(3).Dexp(1).min1(d+1)= min1;
|
|
Exp(1).Dexp(1).max1(d+1)= max1; Exp(2).Dexp(1).max1(d+1)= max1; Exp(3).Dexp(1).max1(d+1)= max1;
|
|
|
|
else
|
|
% Pick the first spot with zeros
|
|
medianCalcFailed= 'To Few nonZero spots for valid median RF1 selection'
|
|
firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
|
|
Exp(1).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(2).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(3).Dexp(1).RFmd1indx(d+1)=firstZero;
|
|
Exp(1).Dexp(1).RFmd1pltN= RF1mp; Exp(2).Dexp(1).RFmd1pltN= RF1mp; Exp(3).Dexp(1).RFmd1pltN= RF1mp; %EZdestComp uses the masterplate number to get all the destPlates scanNumbers
|
|
|
|
try, medValList1{d+1}= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch end
|
|
|
|
|
|
end
|
|
catch %try ~ln219
|
|
medianCalcTryFailed1= 'Failed! Failed! But process continued with bogus P1ind384 spot value!'
|
|
|
|
try
|
|
firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
|
|
Exp(1).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(2).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(3).Dexp(1).RFmd1indx(d+1)=firstZero;
|
|
catch
|
|
catchissue='Ln328'
|
|
Exp(1).Dexp(1).RFmd1indx(d+1)=384; Exp(2).Dexp(1).RFmd1indx(d+1)=384; Exp(3).Dexp(1).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
|
|
end
|
|
try
|
|
Exp(1).Dexp(1).RFmd1pltN= RF1mp; Exp(2).Dexp(1).RFmd1pltN= RF1mp; Exp(3).Dexp(1).RFmd1pltN= RF1mp;
|
|
catch
|
|
catchissue='Ln334'
|
|
Exp(1).Dexp(1).RFmd1pltN= 1; Exp(2).Dexp(1).RFmd1pltN= 1; Exp(3).Dexp(1).RFmd1pltN= 1;
|
|
end
|
|
error='EZvInit after Ln278'
|
|
end %try ~ln219
|
|
|
|
end %for d=0:DMnum
|
|
end % if exist('RF1scanN','var')
|
|
%*************************************************************************************
|
|
|
|
Exp(1).Dexp(1).RFmd2indx=[]; Exp(2).Dexp(1).RFmd2indx=[]; Exp(3).Dexp(1).RFmd2indx=[];
|
|
Exp(1).Dexp(1).RFmd2pltN=[]; Exp(2).Dexp(1).RFmd2pltN=[]; Exp(3).Dexp(1).RFmd2pltN=[];
|
|
|
|
if exist('RF2scanN','var')
|
|
for d=0:(DMnum-1);
|
|
medianIndx2=[];
|
|
nonZeroIndx2=[];
|
|
medValList2=[];
|
|
rf2scN=RF2scanN+d;
|
|
|
|
try %if RF2scanN doesn't exist this addition to list will be skipped
|
|
nonZeroIndx2= find(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5));
|
|
if isempty(nonZeroIndx2), nonZeroCnt2=0; medianIndx2= nonZeroIndx2;
|
|
else nonZeroCnt2=length(nonZeroIndx2);
|
|
end
|
|
%
|
|
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2= nonZeroIndx2(1:nonZeroCnt2-1); end
|
|
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2= nonZeroIndx2; end
|
|
if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
|
|
medValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);
|
|
medValList2{d+1}= medValLst2;
|
|
min2= min(medValLst2);
|
|
max2= max(medValLst2);
|
|
std2= std(medValLst2)
|
|
mean2= mean(medValLst2);
|
|
mval2=median(medValLst2) %(Exp(expN).Dexp(1).scan(RF2scanN).plate(1).CFout(1:383,5));
|
|
RFmd2pos=find(mval2==(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5)));
|
|
RFmd2loc(1)= ceil(RFmd2pos/24); %calc r value
|
|
RFmd2loc(2)= RFmd2pos - ((RFmd2loc(1)-1)*24); %calc c value
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
aa(lstindx,1)= {strcat('RF2md(',num2str(d+1),')')}; %{'RF2md'};
|
|
aa(lstindx,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,' std~',num2str(std2))};
|
|
bb(lstindxOrf,1)= {strcat('RF2md(',num2str(d+1),')')}; %{'RF2md'};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,' std~',num2str(std2))};
|
|
|
|
Exp(1).Dexp(1).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(1).Dexp(1).RFmd2indx(d+1)=RFmd2pos; Exp(2).Dexp(1).RFmd2indx(d+1)=RFmd2pos; Exp(3).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
|
|
Exp(1).Dexp(1).RFmd2pltN= RF2mp; Exp(2).Dexp(1).RFmd2pltN= RF2mp; Exp(3).Dexp(1).RFmd2pltN= RF2mp;
|
|
Exp(1).Dexp(1).RFmd2val(d+1)= mval2; Exp(2).Dexp(1).RFmd2val(d+1)= mval2; Exp(3).Dexp(1).RFmd2val(d+1)= mval2;
|
|
Exp(1).Dexp(1).mean2(d+1)= mean2; Exp(2).Dexp(1).mean2(d+1)= mean2; Exp(3).Dexp(1).mean2(d+1)= mean2;
|
|
Exp(1).Dexp(1).std2(d+1)= std2; Exp(2).Dexp(1).std2(d+1)= std2; Exp(3).Dexp(1).std2(d+1)= std2;
|
|
Exp(1).Dexp(1).min2(d+1)= min2; Exp(2).Dexp(1).min2(d+1)= min2; Exp(3).Dexp(1).min2(d+1)= min2;
|
|
Exp(1).Dexp(1).max2(d+1)= max2; Exp(2).Dexp(1).max2(d+1)= max2; Exp(3).Dexp(1).max2(d+1)= max2;
|
|
|
|
else
|
|
% Pick the first spot with zeros
|
|
% Use that position to satisfy and keep process OK
|
|
medianCalcFailed2= 'To Few nonZero spots for valid median RF2 selection'
|
|
firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')
|
|
Exp(1).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(2).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(3).Dexp(1).RFmd2indx(d+1)=firstZero2;
|
|
Exp(1).Dexp(1).RFmd2pltN= RF2mp; Exp(2).Dexp(1).RFmd2pltN= RF2mp; Exp(3).Dexp(1).RFmd2pltN= RF2mp;
|
|
|
|
try, medValList2(d+1)= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5); nonZeroCnt2; catch end
|
|
|
|
end
|
|
|
|
catch
|
|
medianCalcTryFailed2= 'Failed! Failed! No RF1median But process continued with bogus P1ind384 spot value!'
|
|
|
|
try
|
|
firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')
|
|
Exp(1).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(2).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(3).Dexp(1).RFmd2indx(d+1)=firstZero2;
|
|
catch
|
|
catchissue='Ln402'
|
|
Exp(1).Dexp(1).RFmd2indx(d+1)=384; Exp(2).Dexp(1).RFmd2indx(d+1)=384; Exp(3).Dexp(1).RFmd2indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
|
|
end
|
|
try
|
|
Exp(1).Dexp(1).RFmd2pltN= RF2mp; Exp(2).Dexp(1).RFmd2pltN= RF2mp; Exp(3).Dexp(1).RFmd2pltN= RF2mp;
|
|
catch
|
|
catchissue='Ln408'
|
|
Exp(1).Dexp(1).RFmd2pltN= 1; Exp(2).Dexp(1).RFmd2pltN= 1; Exp(3).Dexp(1).RFmd2pltN= 1;
|
|
end
|
|
error='EZexpSel lineAfter 354'
|
|
end %if RF2scanN doesn't exist this addition to list will be skipped
|
|
RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
|
|
Exp(1).Dexp(1).RFmean(d+1)= mean(RFcombValList);Exp(2).Dexp(1).RFmean(d+1)= mean(RFcombValList);Exp(3).Dexp(1).RFmean(d+1)= mean(RFcombValList);
|
|
Exp(1).Dexp(1).RFstd(d+1)=std(RFcombValList);Exp(2).Dexp(1).RFstd(d+1)=std(RFcombValList);Exp(3).Dexp(1).RFstd(d+1)=std(RFcombValList);
|
|
Exp(1).Dexp(1).RFmin(d+1)=min(RFcombValList);Exp(2).Dexp(1).RFmin(d+1)=min(RFcombValList);Exp(3).Dexp(1).RFmin(d+1)=min(RFcombValList);
|
|
Exp(1).Dexp(1).RFmax(d+1)=max(RFcombValList);Exp(2).Dexp(1).RFmax(d+1)=max(RFcombValList);Exp(3).Dexp(1).RFmax(d+1)=max(RFcombValList);
|
|
|
|
%can delete the following redundant line of code
|
|
Exp(2).Dexp(1).RFmean(d+1)= Exp(1).Dexp(1).RFmean(d+1); Exp(3).Dexp(1).RFmean(d+1)= Exp(1).Dexp(1).RFmean(d+1);
|
|
|
|
end %for d=0:DMnum
|
|
elseif exist('RF1scanN','var')
|
|
Exp(1).Dexp(1).RFmean= Exp(1).Dexp(1).mean1; Exp(2).Dexp(1).RFmean= Exp(2).Dexp(1).mean1; Exp(3).Dexp(1).RFmean= Exp(3).Dexp(1).mean1;
|
|
Exp(1).Dexp(1).RFstd= Exp(1).Dexp(1).std1; Exp(2).Dexp(1).RFstd= Exp(2).Dexp(1).std1; Exp(3).Dexp(1).RFstd= Exp(3).Dexp(1).std1;
|
|
Exp(1).Dexp(1).RFmin= Exp(1).Dexp(1).min1; Exp(2).Dexp(1).RFmin= Exp(2).Dexp(1).min1; Exp(3).Dexp(1).RFmin= Exp(3).Dexp(1).min1;
|
|
Exp(1).Dexp(1).RFmax= Exp(1).Dexp(1).max1; Exp(2).Dexp(1).RFmax= Exp(2).Dexp(1).max1; Exp(3).Dexp(1).RFmax= Exp(3).Dexp(1).max1;
|
|
end %if exist('RF2scanN','var')
|
|
|
|
%*************************************************************************************************
|
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
|
%*************************************************************************************************
|
|
%***********DISPERSE REFERENCE PLATES
|
|
Exp(expN).Dexp(1).RFmdPindx=[];
|
|
Exp(expN).Dexp(1).RFmdPpltN=[];
|
|
if exist('drf','var') %('RF1scanN','var')
|
|
%Det. index of change from one MP to the next
|
|
|
|
i=2;
|
|
chgIndx(1)=1;
|
|
for j=1:length(drf(:,3))
|
|
|
|
if j>1
|
|
if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
|
|
end
|
|
end
|
|
chgIndx(length(chgIndx)+1)= length(drf)+1;
|
|
uu=zeros(size(drf,1),4);
|
|
uu(:,1:4)= cell2mat(drf(:,3:6));
|
|
vv= zeros(length(drf),DMnum);
|
|
%************************************
|
|
dMPs= unique(cell2mat(drf(:,3)));
|
|
%*****************************************
|
|
|
|
for mm=1:length(dMPs)
|
|
|
|
for d=1:(DMnum)
|
|
medianIndxDisp=[];
|
|
NZrefIndxP=[];
|
|
nonZeroValsP=[];
|
|
medValLstDisp=[];
|
|
rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
|
|
|
|
try % Determine the dispersed RFs median mean and std if such exist
|
|
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));
|
|
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
nonZeroValsP= nonzeros(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
|
|
minDisp= min(nonZeroValsP);
|
|
maxDisp= max(nonZeroValsP);
|
|
std1Disp= std(nonZeroValsP);
|
|
mean1Disp= mean(nonZeroValsP);
|
|
drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
|
|
%MEDIAN Determination for PLATES with Dispersed RFs
|
|
if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP;
|
|
else nonZeroCntDisp=length(NZrefIndxP);
|
|
end
|
|
|
|
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp= NZrefIndxP(1:nonZeroCntDisp-1); end
|
|
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end
|
|
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
|
|
medValLstDisp= Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
|
|
mval1Disp=median(medValLstDisp);
|
|
nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);
|
|
RFmd1posD= NZrefIndxP(nonZeroMedPosIndx);
|
|
RFmd1locD(1)= ceil(RFmd1posD/24); %calc r value
|
|
RFmd1locD(2)= RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
|
|
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
aa(lstindx,1)= {strcat('RF1mdP(',num2str(d),')')}; %{'RF1md'};
|
|
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))}; %,'std_',num2str(std1))};
|
|
bb(lstindxOrf,1)= {strcat('RF1mdP(',num2str(d),')')}; %{'RF1md'};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))}; %,'std_',num2str(std1))};
|
|
|
|
Exp(1).Dexp(1).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(1).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD; Exp(2).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD; Exp(3).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD;
|
|
Exp(1).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm); Exp(2).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm); Exp(3).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
|
|
Exp(1).Dexp(1).RFmedianP(d,dMPs(mm))= mval1Disp; Exp(2).Dexp(1).RFmedianP(d,dMPs(mm))= mval1Disp; Exp(3).Dexp(1).RFmedianP(d,dMPs(mm))= mval1Disp;
|
|
Exp(1).Dexp(1).meanP(d,dMPs(mm))= mean1Disp; Exp(2).Dexp(1).meanP(d,dMPs(mm))= mean1Disp; Exp(3).Dexp(1).meanP(d,dMPs(mm))= mean1Disp;
|
|
Exp(1).Dexp(1).stdP(d,dMPs(mm))= std1Disp; Exp(2).Dexp(1).stdP(d,dMPs(mm))= std1Disp; Exp(3).Dexp(1).stdP(d,dMPs(mm))= std1Disp;
|
|
Exp(1).Dexp(1).minP(d,dMPs(mm))= minDisp; Exp(2).Dexp(1).minP(d,dMPs(mm))= minDisp; Exp(3).Dexp(1).minP(d,dMPs(mm))= minDisp;
|
|
Exp(1).Dexp(1).maxP(d,dMPs(mm))= maxDisp; Exp(2).Dexp(1).maxP(d,dMPs(mm))= maxDisp; Exp(3).Dexp(1).maxP(d,dMPs(mm))= maxDisp;
|
|
|
|
else
|
|
% Need to set L r K values to zeros or pick the first spot with zeros
|
|
%Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
|
|
medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection'
|
|
firstZeroDindx= find(((Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
|
|
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
|
|
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroD;
|
|
Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
|
|
|
|
|
|
end %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 ln584
|
|
catch %try ln565
|
|
medianCalcTryFailed1D= 'Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
|
|
|
|
try
|
|
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first')
|
|
firstZeroPindx= uu(firstZeroindxD,4);
|
|
Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
|
|
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
|
|
|
|
catch
|
|
catchissue='try at Ln565'
|
|
Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
|
|
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
|
|
end
|
|
try
|
|
Exp(expN).Dexp(1).RFmdPpltN= dMPs(mm);
|
|
catch
|
|
catchissue='Ln'
|
|
Exp(expN).Dexp(1).RFmdPpltN= 1; %This might keep from breaking BUT ???
|
|
end
|
|
error='EZexpSel lineAfter 565'
|
|
end %try ~ln565
|
|
|
|
end %for d=0:DMnum
|
|
end %for mm=1:length(dMPs)
|
|
|
|
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
|
|
uu= horzcat(uu,vv);
|
|
for d=1:DMnum
|
|
medianIndxD=[];
|
|
NZrfIndxG=[];
|
|
minG = min(nonzeros(vv(:,d)));
|
|
maxG = max(nonzeros(vv(:,d)));
|
|
RFmeanG=mean(nonzeros(vv(:,d)));
|
|
RFstdG= std(nonzeros(vv(:,d)));
|
|
NZrfIndxG= find(nonzeros(vv(:,d)));
|
|
|
|
if isempty(RFmeanG), nonZeroCntD=0;
|
|
else nonZeroCntD= length(nonzeros(vv(:,d)));
|
|
end
|
|
%Calc. of median requires an odd number of indx items
|
|
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD= NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
|
|
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD= NZrfIndxG(:); end
|
|
|
|
if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
|
|
|
|
mvalsDG= median(vv(medianIndxD,d)); %(nonzeros(vv(:,d)));
|
|
nzPosIndxDG=find(mvalsDG==vv(:,d));
|
|
RFmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
|
|
RFmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
|
|
RFmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
aa(lstindx,1)= {strcat('RF1mdG(',num2str(d),')')};
|
|
aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
|
|
bb(lstindxOrf,1)= {strcat('RF1mdG(',num2str(d),')')};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
|
|
|
|
Exp(1).Dexp(1).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(1).Dexp(1).RFmdGindx(d)=nzPosIndxDG; Exp(2).Dexp(1).RFmdGindx(d)=nzPosIndxDG; Exp(3).Dexp(1).RFmdGindx(d)=nzPosIndxDG;
|
|
Exp(1).Dexp(1).RFmdGpltN(d)= RFmdDGloc(d,1); Exp(2).Dexp(1).RFmdGpltN(d)= RFmdDGloc(d,1); Exp(3).Dexp(1).RFmdGpltN(d)= RFmdDGloc(d,1);
|
|
Exp(1).Dexp(1).RFmdGscanN(d)= uu(nzPosIndxDG,4); Exp(2).Dexp(1).RFmdGscanN(d)= uu(nzPosIndxDG,4); Exp(3).Dexp(1).RFmdGscanN(d)= uu(nzPosIndxDG,4);
|
|
Exp(1).Dexp(1).RFmedianG(d)= mvalsDG; Exp(2).Dexp(1).RFmedianG(d)= mvalsDG; Exp(3).Dexp(1).RFmedianG(d)= mvalsDG;
|
|
Exp(1).Dexp(1).RFmeanG(d)= RFmeanG; Exp(2).Dexp(1).RFmeanG(d)= RFmeanG; Exp(3).Dexp(1).RFmeanG(d)= RFmeanG;
|
|
Exp(1).Dexp(1).RFstdG(d)= RFstdG; Exp(2).Dexp(1).RFstdG(d)= RFstdG; Exp(3).Dexp(1).RFstdG(d)= RFstdG;
|
|
Exp(1).Dexp(1).RFminG(d)= minG; Exp(2).Dexp(1).RFminG(d)= minG; Exp(3).Dexp(1).RFminG(d)= minG;
|
|
Exp(1).Dexp(1).RFmaxG(d)= maxG; Exp(2).Dexp(1).RFmaxG(d)= maxG; Exp(3).Dexp(1).RFmaxG(d)= maxG;
|
|
|
|
|
|
end %if ~isempty(NZrfIndxG(:,d)) && length(medianIndxD) > (.15*size(drf,1))
|
|
end %for d=1:DMnum
|
|
|
|
end % if exist('drf','var')
|
|
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
|
|
%*****************************************************************************************************
|
|
|
|
|
|
|
|
|
|
|
|
|
|
%SORT and build GeneList
|
|
|
|
Exp(1).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
|
|
gnLstRaw= strcat(aa(:,1),aa(:,2));
|
|
Exp(1).Dexp(1).srtGnLst= sort(gnLstRaw);
|
|
Exp(2).Dexp(1).srtGnLst=Exp(1).Dexp(1).srtGnLst;
|
|
Exp(3).Dexp(1).srtGnLst=Exp(1).Dexp(1).srtGnLst;
|
|
orfLstRaw=strcat(bb(:,1),bb(:,2));
|
|
Exp(1).Dexp(1).srtOrfLst= sort(orfLstRaw);
|
|
Exp(2).Dexp(1).srtOrfLst=Exp(1).Dexp(1).srtOrfLst;
|
|
Exp(3).Dexp(1).srtOrfLst=Exp(1).Dexp(1).srtOrfLst;
|
|
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
|
|
catch ME %Outer loop try around entire code subroutine
|
|
cd(w)
|
|
set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {'Check MPDMmat file'};{'Check .xls files'};{'Check \Fotos .mat files'};{'Check \matResults file'}]))
|
|
%Exp(expN).Dexp(1).srtGnLst={('Failed To Load')};
|
|
Exp(1).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
Exp(2).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
Exp(3).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
%Exp(expN).srtOrfLst={('Failed To Load')};
|
|
Exp(1).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
Exp(2).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
Exp(3).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);
|
|
|
|
%[openExpfile,openExppath]
|
|
if isempty(strfind(openExpfile,'.mat'))
|
|
|
|
cd(openExppath)
|
|
cd ..
|
|
ExpPath=pwd;
|
|
cd(w)
|
|
ExpOutImFile= fullfile(openExppath,openExpfile);
|
|
EZvImagesOnly
|
|
end
|
|
|
|
end
|
|
%*********************************************************
|
|
DexpN=1;
|
|
EZdiagRFsSheet %*
|
|
%****************
|
|
Exp(1).Dexp(1).RFrnames=rnames; Exp(2).Dexp(1).RFrnames=rnames; Exp(3).Dexp(1).RFrnames=rnames;
|
|
Exp(1).Dexp(1).RFdata= data; Exp(2).Dexp(1).RFdata= data; Exp(3).Dexp(1).RFdata= data;
|
|
%*********************************************************
|
|
RFconfig=0;
|
|
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
|
|
~isempty(Exp(expN).Dexp(1).RFmean)&&...
|
|
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
|
|
isempty(Exp(expN).Dexp(1).RFmeanG)
|
|
RFconfig=1;
|
|
end
|
|
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))==0 ||...
|
|
isempty(Exp(expN).Dexp(1).RFmean)&&...
|
|
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
|
|
~isempty(Exp(expN).Dexp(1).RFmeanG)
|
|
RFconfig=2;
|
|
end
|
|
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
|
|
~isempty(Exp(expN).Dexp(1).RFmean)&&...
|
|
sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
|
|
~isempty(Exp(expN).Dexp(1).RFmeanG)
|
|
RFconfig=3;
|
|
end
|
|
Exp(1).RFconfig= RFconfig; Exp(2).RFconfig= RFconfig; Exp(3).RFconfig= RFconfig; %ZoneRelated
|
|
%*****************************
|
|
try msgBadGeneName, catch, end
|
|
try
|
|
Exp(1).resetHtmpTg =3; Exp(2).resetHtmpTg =3; Exp(3).resetHtmpTg =3; %ZoneRelated
|
|
if RFconfig==0,
|
|
RFconfigMsg= 'No RF1 references in this Experiment Job'
|
|
Exp(1).resetHtmpTg =1; Exp(2).resetHtmpTg =1; Exp(3).resetHtmpTg =1; %ZoneRelated
|
|
end
|
|
catch
|
|
end
|
|
|
|
%*****************************
|
|
% HtMapTog 'string', 'Current user HL/HN' selection'
|
|
try
|
|
Exp(1).htmapPBsel=0;
|
|
set(handles.HtMapTog1,'string','HL')
|
|
|
|
Exp(2).htmapPBsel=0; %ZoneRelated
|
|
set(handles.HtMapTog2,'string','HL')
|
|
|
|
Exp(3).htmapPBsel=0;
|
|
set(handles.HtMapTog3,'string','HL')
|
|
|
|
catch
|
|
% expN=1;
|
|
end
|
|
|
|
htMapTogPBfg=0;
|
|
Exp(1).htmapRFanswer= {'G','L'}; %ZoneRelated
|
|
Exp(2).htmapRFanswer= {'G','L'};
|
|
Exp(3).htmapRFanswer= {'G','L'};
|
|
|
|
|
|
|