224 lines
9.3 KiB
Matlab
Executable File
224 lines
9.3 KiB
Matlab
Executable File
%EZusrSelRef
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%User Select Reference Diaglog Box
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try
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if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var') %change || &&
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%{
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prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
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'Enter GeneName of Your Reference:'};
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rfMPstr= cell2mat(answer(1));
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rfMPcomas=strfind((cell2mat(answer(1))),',');
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n=0;
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if isempty(rfMPcomas)|| max(rfMPcomas)== length(rfMPstr)
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usrMPs= rfMPstr
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else
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for i= rfMPcomas,
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n=n+1
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usrMPs(n)= str2double(rfMPstr(i-1:i))
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if i== max(rfMPcomas)
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usrMPs(n+1)= str2double(rfMPstr(i:end))
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end
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end
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end
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usrMPs= answer(1);
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refGene= answer(2);
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%}
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prompt={'Enter GeneName to use as Reference:',...
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'Enter Specifics Term if used to futher specify Reference '}
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dlg_title='User Reference Input';
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num_lines=1;
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def={'None','Specifics Term'};
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answer=inputdlg(prompt,dlg_title,num_lines,def);
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rfGenestr= cell2mat(answer(1));
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rfSpec= cell2mat(answer(2));
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end
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%try
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for mp=1:length(Exp(expN).Dexp(DexpN).MP)
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for ind384=1:384
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spN=spN+1;
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end
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%catch
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%end %try for user selected Reference routine
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end
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%***********DISPERSE REFERENCE PLATES
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Exp(expN).Dexp(DexpN).RFmdPindx=[];
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Exp(expN).Dexp(DexpN).RFmdPpltN=[];
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if exist('drf','var') %('RF1scanN','var')
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%Det. index of change from one MP to the next
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i=2;
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chgIndx(1)=1;
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for j=1:length(drf(:,3))
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if j>1
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if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
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end
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end
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chgIndx(length(chgIndx)+1)= length(drf)+1;
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uu=zeros(size(drf,1),4);
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uu(:,1:4)= cell2mat(drf(:,3:6))
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vv= zeros(length(drf),DMnum);
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%************************************
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dMPs= unique(cell2mat(drf(:,3)));
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%*****************************************
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%{
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for mm=1:MPnum
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nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
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end
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%}
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%nzValsG= zeros(DMnum,size(drf,1));
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%nzValsAcc= zeros(DMnum,384);
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for mm=1:length(dMPs) % length(chgIndx)
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for d=1:(DMnum)
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medianIndxDisp=[];
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NZrefIndxP=[];
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nonZeroValsP=[];
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medValLstDisp=[];
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rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
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try % Determine the dispersed RFs median mean and std if such exist
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NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
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%vv= Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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nonZeroValsP= nonzeros(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
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std1Disp= std(nonZeroValsP);
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mean1Disp= mean(nonZeroValsP);
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minDisp= min(nonZeroValsP);
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maxDisp= max(nonZeroValsP);
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drfVals=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
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%nzValsAcc(mm).DM(d,:)= nonZeroValsP;
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%MEDIAN Determination for PLATES with Dispersed RFs
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%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
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if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP;
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else nonZeroCntDisp=length(NZrefIndxP);
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end
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if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp= NZrefIndxP(1:nonZeroCntDisp-1); end
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if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end
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if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
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medValLstDisp= Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
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%medValList1Disp{d}= medValLstDisp;
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mval1Disp=median(medValLstDisp); %mval1=median(Exp(expN).Dexp(DexpN).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
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nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); %(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))); %(nonZeroIndxDisp,5))); %((nonZrfIndx.mp{dMPs(mm),:}),5)));
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RFmd1posD= NZrefIndxP(nonZeroMedPosIndx); %drfPindx((RFmd1posIndx),dMPs(mm));
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RFmd1locD(1)= ceil(RFmd1posD/24); %calc r value
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RFmd1locD(2)= RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
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lstindx=lstindx+1;
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lstindxOrf= lstindxOrf+1;
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aa(lstindx,1)= {strcat('RF1mdP(',num2str(d),')')};
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aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
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bb(lstindxOrf,1)= {strcat('RF1mdP(',num2str(d),')')};
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bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
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Exp(expN).Dexp(DexpN).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))= RFmd1posD;
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
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Exp(expN).Dexp(DexpN).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
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Exp(expN).Dexp(DexpN).RFmedianP(d,dMPs(mm))= mval1Disp;
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Exp(expN).Dexp(DexpN).stdP(d,dMPs(mm))= std1Disp;
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Exp(expN).Dexp(DexpN).meanP(d,dMPs(mm))= mean1Disp;
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Exp(expN).Dexp(DexpN).minP(d,dMPs(mm))= minDisp;
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Exp(expN).Dexp(DexpN).maxP(d,dMPs(mm))= maxDisp;
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else
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% Need to set L r K values to zeros or pick the first spot with zeros
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%Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
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medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection'
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firstZeroDindx= find(((Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
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firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroD;
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
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end %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 ln584
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catch %try ln565
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medianCalcTryFailed1D= 'Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
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try
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firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
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firstZeroPindx= uu(firstZeroindxD,4);
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
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catch
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catchissue='try at Ln565'
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Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
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Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
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end
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try
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Exp(expN).Dexp(DexpN).RFmdPpltN= dMPs(mm);
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catch
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catchissue='Ln619'
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Exp(expN).Dexp(DexpN).RFmdPpltN= 1; %This might keep from breaking BUT ???
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end
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error='EZexpSel lineAfter 565'
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end %try ~ln565
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end %for d=0:DMnum
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end %for mm=1:length(dMPs)
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%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
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uu= horzcat(uu,vv);
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for d=1:DMnum
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medianIndxG=[];
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NZrfIndxG=[];
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minG=min(nonzeros(vv(:,d)));
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maxG=max(nonzeros(vv(:,d)));
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RFmeanG= mean(nonzeros(vv(:,d)));
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RFstdG= std(nonzeros(vv(:,d)));
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NZrfIndxG= find(nonzeros(vv(:,d)));
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if isempty(RFmeanG), nonZeroCntD=0, %medianIndxDisp= RFmeanG(d);
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else nonZeroCntD= length(nonzeros(vv(:,d)));
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end
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%Calc. of median requires an odd number of indx items
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if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD= NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
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if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD= NZrfIndxG(:); end
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if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
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mvalsDG= median(vv(medianIndxD,d)); %(nonzeros(vv(:,d)));
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nzPosIndxDG=find(mvalsDG==vv(:,d));
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RFmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
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RFmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
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RFmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
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lstindx=lstindx+1;
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lstindxOrf= lstindxOrf+1;
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aa(lstindx,1)= {strcat('RF1mdG(',num2str(d),')')};
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aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
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bb(lstindxOrf,1)= {strcat('RF1mdG(',num2str(d),')')};
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bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
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Exp(expN).Dexp(DexpN).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
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Exp(expN).Dexp(DexpN).RFmdGindx(d)= nzPosIndxDG;
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Exp(expN).Dexp(DexpN).RFmdGpltN(d)= RFmdDGloc(d,1);
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Exp(expN).Dexp(DexpN).RFmdGscanN(d)= uu(nzPosIndxDG,4);
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Exp(expN).Dexp(DexpN).RFmedianG(d)= mvalsDG;
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Exp(expN).Dexp(DexpN).RFminG(d)= minG;
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Exp(expN).Dexp(DexpN).RFmaxG(d)= maxG;
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Exp(expN).Dexp(DexpN).RFstdG(d)= RFstdG;
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Exp(expN).Dexp(DexpN).RFmeanG(d)= RFmeanG;
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end
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end
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end % if exist('drf','var')
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%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
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%*********************************************************************
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catch
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msg= 'Failed attempt to apply User Selected Reference'
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end %if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var')
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