1126 lines
49 KiB
Matlab
Executable File
1126 lines
49 KiB
Matlab
Executable File
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global Expaa
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global Expbb
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global expType
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global scansDir
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global zonePB
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w=pwd;
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% Single Exp or Chronological Study
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% Construct a questdlg with three options
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Exp(expN).expLoadCnt=0;
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% Initiation for composite plotting cPlots
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Exp(expN).cTraceN=1;
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Exp(expN).cTraceIndx=1;
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Exp(expN).CompositPlot=0;
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choice='Cancel';
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expType=0;
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choice=questdlg('Choose Single Exp, Chronological Study OR Multi Exp', ...
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'Experiment Type Menu', ...
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'Single Exp','Chronological Study','Multi Exp','Single Exp');
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% Handle response
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switch choice
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case 'Single Exp'
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disp([choice 'Single Exp Selected'])
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expType=1;
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case 'Chronological Study'
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disp([choice 'Chronological Study Selected'])
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expType=2;
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case 'Multi Exp'
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disp([choice 'Multi Exp Selected'])
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expType=3;
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case 'Cancel'
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disp('Cancel Load Exp')
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expType=0
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end
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fprintf('expType=%d\n',expType);
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if expType==0, return; end
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zonePB=expN;
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% Pre Load setup incase failure to Load occurs
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% updated 230818 to migrate to AppDesigner
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if expN==1
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set(handles.zonePB1,'value',1);
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set(handles.zonePB2,'value',0);
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set(handles.zonePB3,'value',0);
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set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6]);
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set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
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set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
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end
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if expN==2
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set(handles.zonePB2,'value',1);
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set(handles.zonePB1,'value',0);
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set(handles.zonePB3,'value',0);
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set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6]);
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set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
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set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
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end
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if expN==3
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set(handles.zonePB3,'value',1);
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set(handles.zonePB1,'value',0);
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set(handles.zonePB2,'value',0);
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set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
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set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
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set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
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end
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Exp(expN).htmapRFanswer={'G','L'}; %ZoneData
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if expType==1
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Exp(expN).DexpType='single';
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% Test for Bad MP cell array (usually 384 [NaN}'s)
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% replaced length(Exp(expN).Dexp(1).MP) with MPnum
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for mx=1:length(Exp(expN).Dexp(1).MP)
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try
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char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))
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MPnum=mx;
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catch
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break
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end
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end
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datacursormode off;
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% Return without execution if user cancels or doesn't select a .mat file
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try
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if matFile==0 || scansDir==0
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return
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end
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catch
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end
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if expN==1 || expN==2 || expN==3
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orfLstSel=get(handles.GeneOrfTog,'value')
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end
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Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
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Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
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set(handles.listboxGnOrf,'value',1) %Fix accomodation for bug in App Designer .. .wlapp converter 230906
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set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
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load(matFile);
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cd(scansDir)
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cd ..;
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resDir=pwd;
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Exp(expN).Dexp(1).resDir=resDir;
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cd ..;
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try % this try-catch is to go up one more dir if the images aren't found (from /OtherResults)
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test4imageDir=imread(fullfile(pwd,'1','1.bmp'));
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ExpPath=pwd;
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Exp(expN).Dexp(1).ExpFoldr=ExpPath;
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catch
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try
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cd ..
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test4imageDir=imread(fullfile(pwd,'1','1.bmp'));
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ExpPath=pwd;
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Exp(expN).Dexp(1).ExpFoldr=ExpPath;
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catch
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cd(w)
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end
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end
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cd(w)
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% Experiment Loads
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% load (fullfile(ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
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load(fullfile(Exp(expN).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
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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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load(fullfile(resDir,'PTmats','NImParameters'))
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%Backup for cond. sothat failure to load is recovered back prev. ExpJob data
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Exp(expN).Dexp(1).temp.DM=DM;
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Exp(expN).Dexp(1).temp.MP=MP;
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Exp(expN).Dexp(1).temp.scan=scan;
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Exp(expN).Dexp(1).temp.FexpScanSpots=FexpScanSpots;
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Exp(expN).Dexp(1).temp.FexpScanBMtp=FexpScanBMtp;
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Exp(expN).Dexp(1).temp.anlZoneRefs=anlZoneRefs;
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Exp(expN).Dexp(1).temp.ImParMat=ImParMat;
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Exp(expN).Dexp(1).DM=Exp(expN).Dexp(1).temp.DM;
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Exp(expN).Dexp(1).MP=Exp(expN).Dexp(1).temp.MP;
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Exp(expN).Dexp(1).scan=Exp(expN).Dexp(1).temp.scan;
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Exp(expN).Dexp(1).FexpScanSpots=Exp(expN).Dexp(1).temp.FexpScanSpots;
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Exp(expN).Dexp(1).FexpScanBMtp=Exp(expN).Dexp(1).temp.FexpScanBMtp;
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Exp(expN).Dexp(1).anlZoneRefs=Exp(expN).Dexp(1).temp.anlZoneRefs;
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Exp(expN).Dexp(1).ImParMat=Exp(expN).Dexp(1).temp.ImParMat;
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Exp(expN).DexpLength=1;
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Exp(expN).Dexp((Exp(expN).DexpLength+1):end)=[];
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% Load new ExpJob
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if expN==1,
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% Exp(1).traceN=0;
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tPtsSize=size(FexpScanBMtp{1,1},3);
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set(handles.MPsldr1,'max',length(MP));
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set(handles.DMsldr1,'max',length(DM.drug));
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set(handles.Tptsldr1,'max',tPtsSize);
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% MPnum=length(Exp(expN).Dexp(1).MP);
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set(handles.MPsldr1,'min',1) %,'max',MPnum+.1)
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DMnum=length(Exp(expN).Dexp(1).DM.drug);
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set(handles.DMsldr1,'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.MPsldr1,'value',1)
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set(handles.DMsldr1,'value',1)
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set(handles.Tptsldr1,'value',1)
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set(handles.MPed1,'string','1')
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set(handles.DMed1,'string','1')
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set(handles.Tpted1,'string','1')
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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.DN1,'value',1)
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set(handles.DN1,'string',1)
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end
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if expN==2,
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%Exp(2).traceN=0;
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tPtsSize=size(FexpScanBMtp{1,1},3);
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set(handles.MPsldr2,'max',length(MP));
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set(handles.DMsldr2,'max',length(DM.drug));
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set(handles.Tptsldr2,'max',tPtsSize);
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%MPnum=length(Exp(expN).Dexp(1).MP);
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set(handles.MPsldr2,'min',1) %,'max',MPnum)
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DMnum=length(Exp(expN).Dexp(1).DM.drug);
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set(handles.DMsldr2,'min',1,'max',DMnum)
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tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
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set(handles.Tptsldr2,'min',1,'max',tPtsSize)
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set(handles.MPsldr2,'value',1)
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set(handles.DMsldr2,'value',1)
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set(handles.Tptsldr2,'value',1)
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set(handles.MPed2,'string','1')
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set(handles.DMed2,'string','1')
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set(handles.Tpted2,'string','1')
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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.DN2,'value',1)
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set(handles.DN2,'string',1)
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end
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if expN==3,
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% Exp(3).traceN=0;
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tPtsSize=size(FexpScanBMtp{1,1},3);
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set(handles.MPsldr3,'max',length(MP));
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set(handles.DMsldr3,'max',length(DM.drug));
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set(handles.Tptsldr3,'max',tPtsSize);
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% MPnum=length(Exp(expN).Dexp(1).MP);
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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.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.Tptsldr3,'min',1,'max',tPtsSize)
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set(handles.MPsldr3,'value',1)
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set(handles.DMsldr3,'value',1)
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set(handles.Tptsldr3,'value',1)
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set(handles.MPed3,'string','1')
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set(handles.DMed3,'string','1')
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set(handles.Tpted3,'string','1')
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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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set(handles.DN3,'value',1)
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set(handles.DN3,'string',1)
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end
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if expN==1,
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set(handles.GeneOrfLoc1,'string',{''});
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set(handles.graphStrLoc1,'string',{''});
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cla(handles.Paxes1);
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end
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if expN==2
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set(handles.GeneOrfLoc2,'string',{''});
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set(handles.graphStrLoc2,'string',{''});
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cla(handles.Paxes2)
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end
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if expN==3
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set(handles.GeneOrfLoc3,'string',{''});
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set(handles.graphStrLoc3,'string',{''})
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cla(handles.Paxes3)
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end
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Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
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Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
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set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtGnLst)
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set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtOrfLst)
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EZVimDisplay
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% Capture Exp Name
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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)-2) +1;
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endPos=(slashPos(length(slashPos)) -1);
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expStrn=xp(startPos:end);
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if expN==1,set(handles.expName1,'string',expStrn);end
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if expN==2,set(handles.expName2,'string',expStrn);end
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if expN==3,set(handles.expName3,'string',expStrn);end
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catch
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catchissue='Ln198'
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end % nested try-catch-end
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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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% Added 17-1023 For User Addition of Gene Composites to ListBox
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Expaa{expN,1}=[];
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Expbb{expN,1}=[];
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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=[];
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RF2mp=[];
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for mp=1:MPnum % length(Exp(expN).Dexp(1).MP)
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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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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'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1'))... %&& mp==1)...
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&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& mp==length(Exp(expN).Dexp(1).MP))...
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&& iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))
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lstindxOrf=lstindxOrf+1;
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Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),':',' ');
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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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%Exp(expN).Dexp(1).mutSpotIndx(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'))... %&& ~RF1fullPlate)...
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&& (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& ~RF2fullPlate)...
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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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Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
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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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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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rfcnt=rfcnt+1;
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RFs(spN:spN+383)=spN:spN+383;
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RF1mp=mp
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RF1scanN=(mp*DMnum)-(DMnum-1)
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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==MPnum ) ...
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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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RF2mp=mp
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RF2scanN=(mp*DMnum)-(DMnum-1)
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% Dispersed Reference capture and find Medians
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elseif strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1') ...
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&& (RF1fullPlate~=1)
|
|
dRF1indx=dRF1indx+1;
|
|
Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
|
|
drf(dRF1indx,1)=(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
|
|
drf(dRF1indx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
|
|
drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)=mp;
|
|
drf(dRF1indx,4)={r}; drfr(dRF1indx,mp)=r;
|
|
drf(dRF1indx,5)={c}; drfc(dRF1indx,mp)=c;
|
|
drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)=ind384;
|
|
end
|
|
catch
|
|
error='EZexpSel lineAfter 236 EZexpSel.m'
|
|
mp
|
|
ind384
|
|
msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
|
|
end
|
|
end
|
|
mp
|
|
end
|
|
|
|
% Cover case if mutorfs RFs are labeled RF1 or RF2
|
|
try
|
|
Exp(expN).Dexp(1).mutSpotIndx.wRFs=union(RFs, mutorfs);
|
|
catch
|
|
msg='No RFs Found in Exp! wRFs'
|
|
Exp(expN).Dexp(1).mutSpotIndx.wRFs=mutorfs;
|
|
end
|
|
try
|
|
Exp(expN).Dexp(1).mutSpotIndx.woRFs=setdiff(mutorfs,RFs);
|
|
catch
|
|
Exp(expN).Dexp(1).mutSpotIndx.woRFs=mutorfs;
|
|
msg='No RFs Found in Exp! woRFs'
|
|
end
|
|
|
|
Exp(expN).Dexp(1).RFmd1indx=[];
|
|
Exp(expN).Dexp(1).RFmd1LB={[]};
|
|
Exp(expN).Dexp(1).RFmd1pltN={};
|
|
Exp(expN).Dexp(1).RFmd1val=[];
|
|
Exp(expN).Dexp(1).mean1=[];
|
|
Exp(expN).Dexp(1).std1=[];
|
|
Exp(expN).Dexp(1).min1=[];
|
|
Exp(expN).Dexp(1).max1=[];
|
|
Exp(expN).Dexp(1).RFcmpK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL=[]; %For Ref Composite 17_1009
|
|
|
|
Exp(expN).Dexp(1).RFmd2indx=[];
|
|
Exp(expN).Dexp(1).RFmd2LB={[]};
|
|
Exp(expN).Dexp(1).RFmd2pltN={};
|
|
Exp(expN).Dexp(1).RFmd2val=[];
|
|
Exp(expN).Dexp(1).mean2=[];
|
|
Exp(expN).Dexp(1).std2=[];
|
|
Exp(expN).Dexp(1).min2=[];
|
|
Exp(expN).Dexp(1).max2=[];
|
|
|
|
Exp(expN).Dexp(1).RFmean=[];
|
|
Exp(expN).Dexp(1).RFstd=[];
|
|
Exp(expN).Dexp(1).RFmin=[];
|
|
Exp(expN).Dexp(1).RFmax=[];
|
|
|
|
Exp(expN).Dexp(1).RFmdPLvals=[]; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFmdPLB={[]};
|
|
Exp(expN).Dexp(1).RFmdPindx=[];
|
|
Exp(expN).Dexp(1).RFmdPpltN=[];
|
|
Exp(expN).Dexp(1).RFmdPscanN=[];
|
|
Exp(expN).Dexp(1).RFmedianP=[];
|
|
Exp(expN).Dexp(1).stdP=[];
|
|
Exp(expN).Dexp(1).meanP=[];
|
|
Exp(expN).Dexp(1).minP=[];
|
|
Exp(expN).Dexp(1).maxP=[];
|
|
Exp(expN).Dexp(1).RFcmpPK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpPr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpPL=[]; %For Ref Composite 17_1009
|
|
|
|
Exp(expN).Dexp(1).RFmdGLB={[]};
|
|
Exp(expN).Dexp(1).RFmdGindx=[];
|
|
Exp(expN).Dexp(1).RFmdGpltN=[];
|
|
Exp(expN).Dexp(1).RFmdGscanN=[];
|
|
Exp(expN).Dexp(1).RFmedianG=[];
|
|
Exp(expN).Dexp(1).RFmeanG=[];
|
|
Exp(expN).Dexp(1).RFstdG=[];
|
|
Exp(expN).Dexp(1).RFminG=[];
|
|
Exp(expN).Dexp(1).RFmaxG=[];
|
|
Exp(expN).Dexp(1).RFcmpGK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGL=[]; %For Ref Composite 17_1009
|
|
|
|
%{
|
|
Exp(expN).Dexp(1).RFmeanGK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFstdGK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFminGK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFmaxGK=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFmeanGr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFstdGr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFminGr=[]; %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFmaxGr=[]; %For Ref Composite 17_1009
|
|
%}
|
|
|
|
|
|
|
|
if exist('RF1scanN','var')
|
|
for d=0:(DMnum-1)
|
|
medianIndx=[];
|
|
nonZeroIndx=[];
|
|
medValList=[];
|
|
rf1scN=RF1scanN+d;
|
|
try % if RF1scanN doesn't exist this addition to list will be skipped
|
|
nonZeroIndx=find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
|
|
if isempty(nonZeroIndx)
|
|
nonZeroCnt=0
|
|
medianIndx=nonZeroIndx;
|
|
else
|
|
nonZeroCnt=length(nonZeroIndx);
|
|
end
|
|
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx=nonZeroIndx(1:nonZeroCnt-1); end
|
|
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx=nonZeroIndx; end
|
|
clear medValLst
|
|
clear kValLst
|
|
clear rValLst
|
|
if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
|
|
medValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5);
|
|
medValList1{d+1}=medValLst;
|
|
min1=min(medValLst);
|
|
max1=max(medValLst);
|
|
std1=std(medValLst);
|
|
mean1=mean(medValLst);
|
|
kValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,3); %For Ref Composite 17_1009
|
|
rValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,4); %For Ref Composite 17_1009
|
|
mval1=median(medValLst); %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
|
|
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),')')}; %{'RF1md'};
|
|
aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
|
|
bb(lstindxOrf,1)={strcat('RF1md(',num2str(d+1),')')}; %{'RF1md'};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
|
|
% Composite Reference Amalgum Plot *********************
|
|
lstindx=lstindx+1;
|
|
lstindxOrf=lstindxOrf+1;
|
|
aa(lstindx,1)={strcat('RF1cmp(',num2str(d+1),')')};
|
|
aa(lstindx,2)={''};
|
|
bb(lstindxOrf,1)={strcat('RF1cmp(',num2str(d+1),')')};
|
|
bb(lstindxOrf,2)={''};
|
|
|
|
Exp(expN).Dexp(1).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(expN).Dexp(1).RFmd1indx(d+1)=RFmd1pos;
|
|
Exp(expN).Dexp(1).RFmd1pltN=RF1mp;
|
|
Exp(expN).Dexp(1).RFmd1val(d+1)=mval1;
|
|
Exp(expN).Dexp(1).RFmd1Lvals=medValLst; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).mean1(d+1)=mean1;
|
|
Exp(expN).Dexp(1).std1(d+1)=std1;
|
|
Exp(expN).Dexp(1).min1(d+1)=min1;
|
|
Exp(expN).Dexp(1).max1(d+1)=max1;
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).Lvals=medValLst; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).med=median(medValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).mean=mean(medValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).std=std(medValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).min=min(medValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).max=max(medValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).Kvals=kValLst; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).med=median(kValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).mean=mean(kValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).std=std(kValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).min=min(kValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).max=max(kValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).rvals=rValLst; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).med=median(rValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).mean=mean(rValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).std=std(rValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).min=min(rValLst); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009
|
|
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
|
|
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(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
|
|
Exp(expN).Dexp(1).RFmd1pltN=RF1mp;
|
|
try
|
|
medValList1{d+1}=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt;
|
|
catch
|
|
catcherror='Ln356'
|
|
end
|
|
end % ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
|
|
catch
|
|
medianCalcTryFailed1='Failed! Failed! Ln362 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(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
|
|
catch
|
|
catchissue='Ln366'
|
|
Exp(expN).Dexp(1).RFmd1indx(d+1)=384; % if crapout,Then use spot384 as default to keep going
|
|
end
|
|
try
|
|
Exp(expN).Dexp(1).RFmd1pltN=RF1mp;
|
|
catch
|
|
catchissue='Ln372'
|
|
Exp(expN).Dexp(1).RFmd1pltN=1;
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
% Calc RF2 median if a full plate of RF2s exist
|
|
Exp(expN).Dexp(1).RFmd2indx=[];
|
|
Exp(expN).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
|
|
clear medValLst2
|
|
clear kValLst2
|
|
clear rValLst2
|
|
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);
|
|
kValLst2=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,3); % for Ref Composite 17_1009
|
|
rValLst2=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,4); % for Ref Composite 17_1009
|
|
mval2=median(medValLst2); %mval2=median(Exp(expN).Dexp(1).scan(RF2mps).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))};
|
|
%Composite Reference Amalgum Plot (CRAP)
|
|
lstindx=lstindx+1;
|
|
lstindxOrf=lstindxOrf+1;
|
|
aa(lstindx,1)={strcat('RF2cmp(',num2str(d+1),')')};
|
|
aa(lstindx,2)={''};
|
|
bb(lstindxOrf,1)={strcat('RF2cmp(',num2str(d+1),')')};
|
|
bb(lstindxOrf,2)={''};
|
|
Exp(expN).Dexp(1).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(expN).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
|
|
Exp(expN).Dexp(1).RFmd2pltN=RF2mp;
|
|
Exp(expN).Dexp(1).RFmd2val(d+1)=mval2;
|
|
Exp(expN).Dexp(1).RFmd1Lvals=medValLst2; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).mean2(d+1)=mean2;
|
|
Exp(expN).Dexp(1).std2(d+1)=std2;
|
|
Exp(expN).Dexp(1).min2(d+1)=min2;
|
|
Exp(expN).Dexp(1).max2(d+1)=max2;
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).Lvals=medValLst2; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).med=median(medValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).mean=mean(medValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).std=std(medValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).min=min(medValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).max=max(medValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).Kvals=kValLst2; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).med=median(kValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).mean=mean(kValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).std=std(kValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).min=min(kValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).max=max(kValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).rvals=rValLst2; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).med=median(rValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).mean=mean(rValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).std=std(rValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).min=min(rValLst2); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009
|
|
else
|
|
% Pick the first spot with zeros
|
|
% Use that position to satisfy and keep process OK
|
|
medianCalcFailed2='Too 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(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
|
|
Exp(expN).Dexp(1).RFmd2pltN=RF2mp;
|
|
try medValList2{d+1}=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5); nonZeroCnt2; catch, catchissue='Ln431', end
|
|
end
|
|
catch
|
|
medianCalcTryFailed2='Failed! Failed! Ln436 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(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
|
|
catch
|
|
Exp(expN).Dexp(1).RFmd2indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
|
|
end
|
|
try
|
|
Exp(expN).Dexp(1).RFmd2pltN=RF2mp;
|
|
catch
|
|
catchissue='Ln448'
|
|
Exp(expN).Dexp(1).RFmd2pltN=1;
|
|
end
|
|
end
|
|
clear RFcombValList
|
|
RFcombValList=cat(1,medValList1{d+1},medValList2{d+1});
|
|
Exp(expN).Dexp(1).RFmean(d+1)=mean(RFcombValList);
|
|
Exp(expN).Dexp(1).RFstd(d+1)=std(RFcombValList);
|
|
try, Exp(expN).Dexp(1).RFmin(d+1)=min(RFcombValList);
|
|
catch, Exp(expN).Dexp(1).RFmin(d+1)=0; end
|
|
try, Exp(expN).Dexp(1).RFmax(d+1)=max(RFcombValList);
|
|
catch, Exp(expN).Dexp(1).RFmax(d+1)=0; end
|
|
end
|
|
elseif exist('RF1scanN','var')
|
|
Exp(expN).Dexp(1).RFmean=Exp(expN).Dexp(1).mean1;
|
|
Exp(expN).Dexp(1).RFstd=Exp(expN).Dexp(1).std1;
|
|
Exp(expN).Dexp(1).RFmin=Exp(expN).Dexp(1).min1;
|
|
Exp(expN).Dexp(1).RFmax=Exp(expN).Dexp(1).max1;
|
|
end
|
|
|
|
% Disperse Reference Plates
|
|
Exp(expN).Dexp(1).RFmdPindx=[];
|
|
Exp(expN).Dexp(1).RFmdPpltN=[];
|
|
if exist('drf','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) % length(chgIndx)
|
|
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)); %find(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
|
|
%vv=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
%For Global Ref Composite 17_1009
|
|
vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
|
|
vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
|
|
nonZeroValsP=nonzeros(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
|
|
std1Disp=std(nonZeroValsP);
|
|
mean1Disp=mean(nonZeroValsP);
|
|
minDisp=min(nonZeroValsP);
|
|
maxDisp=max(nonZeroValsP);
|
|
drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
|
|
% MEDIAN Determination for PLATES with Dispersed RFs
|
|
% NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
|
|
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);
|
|
% medValList1Disp{d}=medValLstDisp;
|
|
mval1Disp=median(medValLstDisp); % mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
|
|
nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); % (Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))); %(nonZeroIndxDisp,5))); %((nonZrfIndx.mp{dMPs(mm),:}),5)));
|
|
RFmd1posD=NZrefIndxP(nonZeroMedPosIndx); % drfPindx((RFmd1posIndx),dMPs(mm));
|
|
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),')')};
|
|
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
|
|
bb(lstindxOrf,1)={strcat('RF1mdP(',num2str(d),')')};
|
|
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
|
|
|
|
Exp(expN).Dexp(1).RFmdPLvals(d,dMPs(mm))=mval1Disp; %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD;
|
|
Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
|
|
Exp(expN).Dexp(1).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
|
|
Exp(expN).Dexp(1).RFmedianP(d,dMPs(mm))=mval1Disp;
|
|
Exp(expN).Dexp(1).stdP(d,dMPs(mm))=std1Disp;
|
|
Exp(expN).Dexp(1).meanP(d,dMPs(mm))=mean1Disp;
|
|
Exp(expN).Dexp(1).minP(d,dMPs(mm))=minDisp;
|
|
Exp(expN).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
|
|
catch
|
|
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='Ln619'
|
|
Exp(expN).Dexp(1).RFmdPpltN=1; %This might keep from breaking BUT ???
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
% Calc. Global Mean, Std, And Median For Distributed References
|
|
uu=horzcat(uu,vv);
|
|
for d=1:DMnum
|
|
medianIndxG=[];
|
|
NZrfIndxG=[];
|
|
minG=min(nonzeros(vv(:,d)));
|
|
maxG=max(nonzeros(vv(:,d)));
|
|
RFmeanG=mean(nonzeros(vv(:,d)));
|
|
RFstdG=std(nonzeros(vv(:,d)));
|
|
NZrfIndxG=find(vv(:,d)); % find(nonzeros(vv(:,d))); WWRONG FOR A WHILE!
|
|
if isempty(RFmeanG)
|
|
nonZeroCntD=0; % medianIndxDisp=RFmeanG(d);
|
|
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))};
|
|
% Composite Reference Amalgum Plot
|
|
lstindx=lstindx+1;
|
|
lstindxOrf=lstindxOrf+1;
|
|
aa(lstindx,1)={strcat('RFcmpG(',num2str(d),')')};
|
|
aa(lstindx,2)={''};
|
|
bb(lstindxOrf,1)={strcat('RFcmpG(',num2str(d),')')};
|
|
bb(lstindxOrf,2)={''};
|
|
% Exp(expN).Dexp(1).RFmdGLvals=vv(medianIndxD,d); %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(expN).Dexp(1).RFmdGindx(d)=nzPosIndxDG;
|
|
Exp(expN).Dexp(1).RFmdGpltN(d)=RFmdDGloc(d,1);
|
|
Exp(expN).Dexp(1).RFmdGscanN(d)=uu(nzPosIndxDG,4);
|
|
Exp(expN).Dexp(1).RFmedianG(d)=mvalsDG;
|
|
Exp(expN).Dexp(1).RFminG(d)=minG;
|
|
Exp(expN).Dexp(1).RFmaxG(d)=maxG;
|
|
Exp(expN).Dexp(1).RFstdG(d)=RFstdG;
|
|
Exp(expN).Dexp(1).RFmeanG(d)=RFmeanG;
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).Lvals=vv(medianIndxD,d); %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).med=median(vv(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).mean=mean(vv(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).std=std(vv(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).min=min(vv(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGL.dm(d).max=max(vv(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).Kvals=vvK(medianIndxD,d); %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).med=median(vvK(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).mean=mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).std=std(vvK(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).min=min(vvK(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGK.dm(d).max=max(vvK(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).rvals=vvr(medianIndxD,d); %17_1201 TrendOL
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).med=median(vvr(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).mean=mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).std=std(vvr(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).min=min(vvr(medianIndxD,d)); %For Ref Composite 17_1009
|
|
Exp(expN).Dexp(1).RFcmpGr.dm(d).max=max(vvr(medianIndxD,d)); %For Ref Composite 17_1009
|
|
end
|
|
end
|
|
end
|
|
|
|
for mp=1:MPnum % length(Exp(expN).Dexp(1).MP)
|
|
for ind384=1:384
|
|
spN=spN+1;
|
|
end
|
|
end
|
|
|
|
gnLstRaw=strcat(aa(:,1),aa(:,2));
|
|
Exp(expN).Dexp(1).srtGnLst=sort(gnLstRaw);
|
|
orfLstRaw=strcat(bb(:,1),bb(:,2));
|
|
Exp(expN).Dexp(1).srtOrfLst=sort(orfLstRaw);
|
|
|
|
% Auto select Zone and load listboxGnOrf data
|
|
zeroCLn=zeros(1,DMnum);
|
|
Exp(expN).expLoadCnt=Exp(expN).expLoadCnt+1; expLdCnt=Exp(expN).expLoadCnt;
|
|
zonePB=expN;
|
|
if expN==1
|
|
set(handles.zonePB1,'value',1)
|
|
set(handles.zonePB2,'value',0)
|
|
set(handles.zonePB3,'value',0)
|
|
set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6])
|
|
set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0])
|
|
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
|
|
orfLstSel=get(handles.GeneOrfTog,'value')
|
|
if orfLstSel==1
|
|
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtOrfLst)
|
|
else
|
|
set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
|
|
end
|
|
DNLaxes1=handles.DNLaxes1; % ZoneRelated
|
|
Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
|
|
end
|
|
|
|
if expN==2
|
|
set(handles.zonePB1,'value',0)
|
|
set(handles.zonePB3,'value',0)
|
|
set(handles.zonePB2,'value',1)
|
|
set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6])
|
|
set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0])
|
|
set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
|
|
orfLstSel=get(handles.GeneOrfTog,'value');
|
|
if orfLstSel==1
|
|
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtOrfLst)
|
|
else
|
|
set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
|
|
end
|
|
DNLaxes2=handles.DNLaxes2; % ZoneRelated
|
|
Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
|
|
end
|
|
|
|
if expN==3
|
|
set(handles.zonePB1,'value',0)
|
|
set(handles.zonePB2,'value',0)
|
|
set(handles.zonePB3,'value',1)
|
|
set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
|
|
set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
|
|
set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
|
|
orfLstSel=get(handles.GeneOrfTog,'value');
|
|
if orfLstSel==1
|
|
set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtOrfLst)
|
|
else
|
|
set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
|
|
end
|
|
DNLaxes3=handles.DNLaxes3; % ZoneRelated
|
|
Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
|
|
end
|
|
|
|
if Exp(4).interacPBsel==0 % if interaction "raw" don't show a center line
|
|
for i=1:Exp(expN).expLoadCnt
|
|
try
|
|
set(Exp(expN).hzeroCLn(i),'visible','off');
|
|
catch
|
|
end
|
|
end
|
|
end
|
|
|
|
EZdiagRFsSheet
|
|
|
|
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(expN).RFconfig=RFconfig; % ZoneRelated
|
|
|
|
if RFconfig~=0
|
|
Exp(expN).Dexp(1).RFrnames=rnames;
|
|
Exp(expN).Dexp(1).RFdata=data;
|
|
Exp(expN).Dexp(1).resetHtmpTg=5; % ZoneRelated
|
|
% HtMapTog 'string', 'Current user L/N' selection'
|
|
Exp(expN).Dexp(1).spotIndx=[];
|
|
if expN==1
|
|
Exp(1).htmapPBsel=0;
|
|
set(handles.HtMapTog1,'string','L')
|
|
EZhtMap
|
|
end
|
|
if expN==2
|
|
Exp(2).htmapPBsel=0;
|
|
set(handles.HtMapTog2,'string','L')
|
|
EZhtMap
|
|
end
|
|
if expN==3,
|
|
Exp(3).htmapPBsel=0;
|
|
set(handles.HtMapTog3,'string','L')
|
|
EZhtMap
|
|
end
|
|
htMapTogPBfg=0;
|
|
elseif RFconfig==0
|
|
RFconfigMsg='No RF1 references in this Experiment Job'
|
|
try
|
|
EZsingleExUserRF
|
|
% EZmultiDayGui
|
|
% cd(w)
|
|
% EZmultiDay
|
|
% EZmultiExLoad
|
|
catch
|
|
RFconfigMsg='No RF1 or User selected references in this Experiment Job'
|
|
Exp(expN).Dexp(1).resetHtmpTg=3; % ZoneRelated
|
|
end
|
|
% Exp(expN).Dexp(1).resetHtmpTg=3; %ZoneRelated
|
|
end
|
|
|
|
%{
|
|
try msgBadGeneName, catch, end
|
|
try
|
|
if RFconfig==0,
|
|
RFconfigMsg='No RF1 references in this Experiment Job'
|
|
Exp(expN).Dexp(1).resetHtmpTg=3; %ZoneRelated
|
|
end
|
|
catch
|
|
end
|
|
%}
|
|
elseif expType==2 %Multiple Experiment from in one Folder extraction
|
|
Exp(expN).DexpType='chrono';
|
|
% Test for Bad MP cell array (usually 384 [NaN}'s)
|
|
% replaced length(Exp(expN).Dexp(1).MP) with MPnum
|
|
for mx=1:length(Exp(expN).Dexp(1).MP)
|
|
try
|
|
char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))
|
|
MPnum=mx;
|
|
catch
|
|
break
|
|
end
|
|
end
|
|
|
|
ww=pwd;
|
|
try EZmultiDayGui; catch ME
|
|
msg=ME.message, cd(ww); end
|
|
try EZmultiDay; catch ME
|
|
msg=ME.message, cd(ww); end
|
|
try EZmultiExLoad; catch ME
|
|
msg=ME.message, cd(ww); end
|
|
elseif expType==3
|
|
Exp(expN).DexpType='multi';
|
|
% Test for Bad MP cell array (usually 384 [NaN}'s)
|
|
% replaced length(Exp(expN).Dexp(1).MP) with MPnum
|
|
for mx=1:length(Exp(expN).Dexp(1).MP)
|
|
try
|
|
char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))
|
|
MPnum=mx;
|
|
catch
|
|
break
|
|
end
|
|
end
|
|
|
|
ww=pwd;
|
|
try EZmultiDayGui; catch ME
|
|
msg=ME.message,cd(ww); end
|
|
try EZmultiDay; catch ME
|
|
msg=ME.message, cd(ww); end
|
|
try EZmultiExLoad; catch ME
|
|
msg=ME.message, cd(ww); end
|
|
else
|
|
disp('Cancel Load Exp')
|
|
end
|
|
|
|
% Deprecated Functions
|
|
%{
|
|
%Exp(expN).Dexp(1).RF1cmpK.[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).std1K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).min1K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).max1K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1)RF1cmpr=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).std1r=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).min1r=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).max1r=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).RF=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).std2K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).min2K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).max2K=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).RF2cmpr=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).std2r=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).min2r=[]; %For Ref Composite 17_1009
|
|
%Exp(expN).Dexp(1).max2r=[]; %For Ref Composite 17_1009
|
|
|
|
%kValList1{d+1}=kValLst; %For Ref Composite 17_1009
|
|
%kmin1=min(kValLst); %For Ref Composite 17_1009
|
|
%kmax1=max(kValLst); %For Ref Composite 17_1009
|
|
%kstd1=std(kValLst); %For Ref Composite 17_1009
|
|
%kmean1=mean(kValLst); %For Ref Composite 17_1009
|
|
%rValList1{d+1}=rValLst; %For Ref Composite 17_1009
|
|
%rmin1=min(rValLst); %For Ref Composite 17_1009
|
|
%rmax1=max(rValLst); %For Ref Composite 17_1009
|
|
%rstd1=std(rValLst); %For Ref Composite 17_1009
|
|
%rmean1=mean(rValLst); %For Ref Composite 17_1009
|
|
%kValList2{d+1}=kValLst2; %For Ref Composite 17_1009
|
|
%kmin2=min(kValLst2); %For Ref Composite 17_1009
|
|
%kmax2=max(kValLst2); %For Ref Composite 17_1009
|
|
%kstd2=std(kValLst2); %For Ref Composite 17_1009
|
|
%kmean2=mean(kValLst2); %For Ref Composite 17_1009
|
|
%rValList2{d+1}=rValLst2; %For Ref Composite 17_1009
|
|
% rmin2=min(rValLst2); %For Ref Composite 17_1009
|
|
%rmax2=max(rValLst2); %For Ref Composite 17_1009
|
|
%rstd2=std(rValLst2); %For Ref Composite 17_1009
|
|
%rmean2=mean(rValLst2); %For Ref Composite 17_1009
|
|
|
|
%User Reference Input Dialog Box used in the multiExperiment Chrono setup
|
|
|
|
prompt={'Enter GeneName to use as Reference:',...
|
|
'Enter Specifics Term if used to futher specify Reference '}
|
|
dlg_title='User Reference Input';
|
|
num_lines=1;
|
|
def={'RF1','None'};
|
|
answer=inputdlg(prompt,dlg_title,num_lines,def);
|
|
rfGene=cell2mat(answer(1));
|
|
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
|
|
rfSpec=answer(2); %if strcmpi(answer(2),'None'), rfSpec=''; end
|
|
rfGnSp=strcat(rfGene,rfSpec);
|
|
|
|
%First user input prototype code
|
|
if ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
|
|
prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
|
|
'Enter GeneName of Your Reference:'};
|
|
dlg_title='User Reference Input';
|
|
num_lines=1;
|
|
def={'Ref MP(s)','USRrefGeneName'};
|
|
answer=inputdlg(prompt,dlg_title,num_lines,def);
|
|
rfMPstr=cell2mat(answer(1));
|
|
rfMPcomas=strfind((cell2mat(answer(1))),',');
|
|
n=0;
|
|
if isempty(rfMPcomas)|| max(rfMPcomas)==length(rfMPstr)
|
|
usrMPs=rfMPstr
|
|
else
|
|
for i=rfMPcomas,
|
|
n=n+1
|
|
usrMPs(n)=str2double(rfMPstr(i-1:i))
|
|
if i==max(rfMPcomas)
|
|
usrMPs(n+1)=str2double(rfMPstr(i:end))
|
|
end
|
|
end
|
|
end
|
|
usrMPs=answer(1);
|
|
refGene=answer(2);
|
|
|
|
end
|
|
%}
|