678 lines
31 KiB
Matlab
Executable File
678 lines
31 KiB
Matlab
Executable File
%***********User find and build composite of Selected Gene Composite and
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%*************Plot it on OLay Plot and Trend plot DNLaxles
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%***************For Chonological Studies (multi Day Studies)
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%Called when Composite_ toggle button is clicked.
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%Data stored for printable Trend Plot production (click [L] in DNLaxes )
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%*********************
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global ghandles
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global Exp
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global exDlst
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global exFolder
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tracN=Exp(expN).traceN;
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n= Exp(expN).DexpN; %Temp input for development
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%UmDayaa= cell(3,n); UmDaybb= cell(3,n);
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patrnN=strfind(selGnOrf{1},':'); %Extract Gene-Orf Name
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selStrNm= char(selGnOrf)
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usrGene= selStrNm(1:(patrnN(1)-1))
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prompt={'Enter Specifics Term if used to futher specify selection '}
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dlg_title='User Specifics Term for Refinement Composite';
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num_lines=1;
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def={'None'};
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answer=inputdlg(prompt,dlg_title,num_lines,def);
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%usrGene= cell2mat(answer(1));
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usrSpec= answer(1);
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usrGnSp= strcat(usrGene,usrSpec);
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if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')}; end
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%if strfind(Exp(expN).UgeneSpLst,usrGnSp), break; end
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Exp(expN).Dexp(n).UsrmdPLB= {[]};
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Exp(expN).Dexp(n).UsrMedianG= [];
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Exp(expN).Dexp(n).UsrminG= [];
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Exp(expN).Dexp(n).UsrmaxG= [];
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Exp(expN).Dexp(n).UsrstdG= [];
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Exp(expN).Dexp(n).UsrmeanG= [];
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Exp(expN).Dexp(n).UsrCmpGL= []; %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK= []; %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGr= []; %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrGLB= {};
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for n=1:Exp(expN).DexpLength %LOOP Thru DayExps
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MPnum=length(Exp(expN).Dexp(n).MP);
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DMnum= length(Exp(expN).Dexp(n).DM.drug);
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tPtsSize= size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3));
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%*********************************
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%lstindx= size(aa,1);
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%lstindxOrf= size(bb,1);
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spN=0;
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rfcnt=0;
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dRF1indx=0;
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%usrGene= cell2mat(usrGene); %user entry of Specifics for Ref selection
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usrSp= cell2mat(usrSpec); %user entry of Specifics for Ref selection
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%*******************************************************
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for mp=1:length(Exp(expN).Dexp(n).MP)
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%RF1fullPlate=0;
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for ind384=1:384
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spN=spN+1;
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try %
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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(n).MP(mp).genename{1}(ind384))==38991,
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Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'};
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elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
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Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '};
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end
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%*****************************************************************
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%DISPersed REFerence capture and find Medians
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if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
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strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp)))...
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|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
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strcmpi(usrSp,'None'))) ),
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dRF1indx=dRF1indx+1;
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Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
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drf(dRF1indx,1)= (Exp(expN).Dexp(n).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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%drf(dRF1indx,7)= (Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
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end %if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...
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%*******************************************************************************
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catch
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error='EZexpSel lineAfter 24 EZmultiGeneLst.m'
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mp %Disable in future to prevent a bomb out OR put into a nested TryCatch
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ind384 %Disable in future to prevent a bomb out OR put into a nested TryCatch
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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(n).MP)
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%*****************************************************
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%************************************************************************************************
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%Exp(expN).Dexp(n).UsrmdPindx=[];
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%Exp(expN).Dexp(n).UsrmdPpltN=[];
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if exist('drf','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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clear chgIndx
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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),1 ); %DMnum);
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%************************************
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dMPs= unique(cell2mat(drf(:,3)));
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%*****************************************
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for mm=1:length(dMPs) % length(chgIndx)
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usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel);
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NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp= NZrefIndxP;
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vv(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
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%For Global Ref Composite 17_1009 %**************************************************************************
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vvK(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
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vvr(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
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%*****************************************************************************************************
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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=dmSel:dmSel
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medianIndxG=[];
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NZusrIndxG=[];
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minG=min(nonzeros(vv(:,d)));
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maxG=max(nonzeros(vv(:,d)));
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usrmeanG= mean(nonzeros(vv(:,d)));
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usrStdG= std(nonzeros(vv(:,d)));
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NZusrIndxG= find(vv(:,d));
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if isempty(usrmeanG), 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 value for composite doesn't require and odd number of Indx items
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medianIndxG= NZusrIndxG(:);
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if ~isempty(NZusrIndxG) && length(medianIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
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Exp(expN).Dexp(n).UsrGLB(d)= usrGnSp; %strcat(aa(lstindx,1),aa(lstindx,2));
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Exp(expN).Dexp(n).UsrLvals= vv(medianIndxG);
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Exp(expN).Dexp(n).UsrKvals= vvK(medianIndxG);
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Exp(expN).Dexp(n).Usrrvals= vvr(medianIndxG);
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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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%####################################################################
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end %for n=1:Exp(expN).DexpLength %Loop thru Dayexps
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Exp(expN).UgeneCnt= Exp(expN).UgeneCnt +1;
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Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)= usrGnSp;
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%#######################################################################
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%***********PLOT Values Selected Gene-Specifics Composite ******************************************try
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smpSz= size(medianIndxG,1);
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K= median(vvK(medianIndxG,dmSel)); Ks= num2str(K); Kstd= std(vvK(medianIndxG,dmSel)); KstdStr= num2str(Kstd);
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r= median(vvr(medianIndxG,dmSel)); rs= num2str(r); rstd= std(vvr(medianIndxG,dmSel)); rstdStr= num2str(rstd);
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l= median(vv(medianIndxG,dmSel)); Ls= num2str(l); Lstd= std(vv(medianIndxG,dmSel)); LstdStr= num2str(Lstd);
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Kl= K - std(vvK(medianIndxG,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
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Ku= K + std(vvK(medianIndxG,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
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rl= r - std(vvr(medianIndxG,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
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ru= r + std(vvr(medianIndxG,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
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lfast= l - std(vv(medianIndxG,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
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lslow= l + std(vv(medianIndxG,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
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try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
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try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
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try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
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pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value'));
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plateNum=(LBmp-1)*destPerMP + pertSel;
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indx=((LBr-1)*24) +LBc
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MP=Exp(zoneSel).Dexp(DexpN).MP;
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try
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t=1:200;
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clear g;
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try
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g= K ./ (1 + exp(-r.* (t - l )));
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gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
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gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
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if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
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if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
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Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
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Exp(1).traceN=Exp(1).traceN+1;
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traceN=Exp(1).traceN;
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end
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if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
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Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
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Exp(2).traceN=Exp(2).traceN+1;
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traceN=Exp(2).traceN;
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end
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if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
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Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
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Exp(3).traceN=Exp(3).traceN+1;
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traceN=Exp(3).traceN;
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end
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plot(plotAxes,t,g);hold (plotAxes,'on');
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plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
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%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
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%Store L R and K valves for Composite [C] plots
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Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
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Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
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%************************************************************************
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try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
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Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
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set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
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catch
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catchissue='Ln100 EZlstBoxExt'
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end %trycatch
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%Get the DM agar description
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if expN==1,DMstr=char(get(handles.DM1,'string'));end
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if expN==2,DMstr=char(get(handles.DM2,'string'));end
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if expN==3,DMstr=char(get(handles.DM3,'string'));end
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gene= usrGnSp; orf= '' %MP(1,LBmp).orf{1,1}(indx);
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geneOrfstr= strcat(gene,'_',orf,'_');
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grfgenestr= strcat(gene,'_',orf,'_');
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%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
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%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
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%graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
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graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
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spotDescrip=strcat(graphStr,'->',DMstr);
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xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
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if ispc,
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slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
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else
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slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).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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Exp(zoneSel).hOLname(traceN)= spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
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Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
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Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
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Exp(zoneSel).hOLplateNum(traceN)= plateNum;
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%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
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if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
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if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
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if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
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if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
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if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
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if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
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catch
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catchissue='Ln141 EZlstBoxExt'
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msg='Error'
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end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
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%{
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% If a specific spot median is ever needed
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%Calc. of EXACT median specific culture requires an odd number of indx items
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if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)==0, medianIndxOdd= NZusrIndxG(1:(size(NZusrIndxG,1)-1)); end
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if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)~=0, medianIndxOdd= NZusrIndxG(:); end
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mvalsDG= median(vv(medianIndxOdd,d)); %(nonzeros(vv(:,d)));
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nzPosIndxDG=find(mvalsDG==vv(:,d));
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Exp(expN).Dexp(n).UsrMedianG(d)= mvalsDG;
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Exp(expN).Dexp(n).UsrminG(d)= minG;
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Exp(expN).Dexp(n).UsrmaxG(d)= maxG;
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Exp(expN).Dexp(n).UsrstdG(d)= usrStdG;
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Exp(expN).Dexp(n).UsrmeanG(d)= usrmeanG;
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%}
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%{
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Exp(expN).Dexp(n).UsrCmpGL.dm(d).med= median(vv(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGL.dm(d).mean= mean(vv(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGL.dm(d).std= std(vv(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGL.dm(d).min= min(vv(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGL.dm(d).max= max(vv(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK.dm(d).med= median(vvK(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK.dm(d).mean= mean(vvK(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK.dm(d).std= std(vvK(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK.dm(d).min= min(vvK(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGK.dm(d).max= max(vvK(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGr.dm(d).med= median(vvr(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGr.dm(d).mean= mean(vvr(medianIndxP,d)); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpGr.dm(d).std= std(vvr(medianIndxP,d)); %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpGr.dm(d).min= min(vvr(medianIndxP,d)); %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpGr.dm(d).max= max(vvr(medianIndxP,d)); %For Ref Composite 17_1026
|
|
%}
|
|
|
|
|
|
%{
|
|
for mm=1:length(dMPs) % length(chgIndx)
|
|
|
|
for d= selDM:selDM %1:(DMnum)
|
|
medianIndxDisp=[];
|
|
NZrefIndxP=[];
|
|
nonZeroValsP=[];
|
|
medValLstDisp=[];
|
|
usrScNdisp=((dMPs(mm)-1)*DMnum)+(d);
|
|
|
|
try % Determine the dispersed User Gene median mean and std if such exist
|
|
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp= NZrefIndxP
|
|
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
%For Global Ref Composite 17_1009 %**************************************************************************
|
|
vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
|
|
vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
|
|
%*****************************************************************************************************
|
|
%{
|
|
nonZeroValsP= nonzeros(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
|
|
std1Disp= std(nonZeroValsP);
|
|
mean1Disp= mean(nonZeroValsP);
|
|
minDisp= min(nonZeroValsP);
|
|
maxDisp= max(nonZeroValsP);
|
|
drfVals=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
|
|
|
|
%nzValsAcc(mm).DM(d,:)= nonZeroValsP;
|
|
|
|
%MEDIAN Determination for PLATES with Dispersed RFs
|
|
%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(n).scan(usrScNdisp).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) > 0 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
|
|
medValLstDisp= Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(medianIndxDisp,5);
|
|
mval1Disp=median(medValLstDisp);
|
|
nzMedPosIndx=find(mval1Disp==nonZeroValsP);
|
|
medianIndxP= NZrefIndxP(nzMedPosIndx);
|
|
%UsrmdlocP(1)= ceil(medianIndxP/24); %calc r value
|
|
%UsrmdlocP(2)= medianIndxP - ((UsrmdlocP(1)-1)*24); %calc c value
|
|
|
|
meanKval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3))));
|
|
meanrval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4))));
|
|
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(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
|
|
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
|
|
%Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroD;
|
|
%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
|
|
|
|
|
|
end %~isempty(NZrefIndxP) && length(medianIndxPisp) > 3 ln584
|
|
catch %try ln565
|
|
medianCalcTryFailed1D= 'Failed! Failed! {Dispersed RF1s}'
|
|
try
|
|
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
|
|
firstZeroPindx= uu(firstZeroindxD,4);
|
|
catch
|
|
end
|
|
end %try ~ln565
|
|
end %for d=0:DMnum
|
|
end %for mm=1:length(dMPs)
|
|
%}
|
|
|
|
%{
|
|
%Code Template taken from EZlstBoxCmpExt.m
|
|
try
|
|
%if RFcmpGFlg==0
|
|
smpSz= size(medianIndxP,1);
|
|
K= median(vvK(medianIndxP,dmSel)); Ks= num2str(K); Kstd= std(vvK(medianIndxP,dmSel)); KstdStr= num2str(Kstd);
|
|
r= median(vvr(medianIndxP,dmSel)); rs= num2str(r); rstd= std(vvr(medianIndxP,dmSel)); rstdStr= num2str(rstd);
|
|
l= median(vv(medianIndxP,dmSel)); Ls= num2str(l); Lstd= std(vv(medianIndxP,dmSel)); LstdStr= num2str(Lstd);
|
|
Kl= K - std(vvK(medianIndxP,dmSel)); %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
|
|
Ku= K + std(vvK(medianIndxP,dmSel)); %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
|
|
rl= r - std(vvr(medianIndxP,dmSel)); %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
|
|
ru= r + std(vvr(medianIndxP,dmSel)); %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
|
|
lfast= l - std(vv(medianIndxP,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
|
|
lslow= l + std(vv(medianIndxP,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
|
|
|
|
try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
|
|
try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
|
|
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
|
|
|
|
|
|
t=1:200;
|
|
clear g;
|
|
|
|
try
|
|
g= K ./ (1 + exp(-r.* (t - l )));
|
|
gSlow= Kl ./ (1 + exp(-rl.* (t - lslow )));
|
|
gFast= Ku ./ (1 + exp(-ru.* (t - lfast )));
|
|
if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
|
|
%tser=(scan(1,plateNum).plate(1).t0Series(:));
|
|
%rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);
|
|
|
|
if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
|
|
Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
|
|
Exp(1).traceN=Exp(1).traceN+1;
|
|
traceN=Exp(1).traceN;
|
|
end
|
|
if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
|
|
Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
|
|
Exp(2).traceN=Exp(2).traceN+1;
|
|
traceN=Exp(2).traceN;
|
|
end
|
|
if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
|
|
Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
|
|
Exp(3).traceN=Exp(3).traceN+1;
|
|
traceN=Exp(3).traceN;
|
|
end
|
|
plot(plotAxes,t,g);hold (plotAxes,'on'); %plot(plotAxes,tser,rawData,'g*');
|
|
plot(plotAxes,t,gSlow,'y'); plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
|
|
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
|
|
%Store L R and K valves for Composite [C] plots
|
|
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
|
|
|
|
Exp(expN).lstd(traceN)= std(vv(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
|
|
Exp(expN).kstd(traceN)= std(vvK(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
|
|
Exp(expN).rstd(traceN)= std(vvr(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
|
|
|
|
|
|
Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;
|
|
Exp(expN).lKl(traceN)= Kl; Exp(expN).Ku(traceN)= Ku;
|
|
Exp(expN).lrl(traceN)= rl; Exp(expN).Ku(traceN)= ru;
|
|
%************************************************************************
|
|
try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end, catch; end
|
|
Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
|
|
set(Exp(zoneSel).hOL(traceN),'color',[1 0 0])
|
|
%Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*'); %No Raw Data, Ref Composite 17_1009
|
|
catch
|
|
catchissue='Ln68 EZlstBoxCmpExt'
|
|
end %trycatch
|
|
|
|
%Get the DM agar description
|
|
%if expN==1,DMstr=char(get(handles.DM1,'string'));end
|
|
%if expN==2,DMstr=char(get(handles.DM2,'string'));end
|
|
%if expN==3,DMstr=char(get(handles.DM3,'string'));end
|
|
DMstr= num2str(dmSel);
|
|
|
|
%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
|
|
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
|
|
%graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
|
|
graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
|
|
spotDescrip=strcat(graphStr,'DMS->',DMstr);
|
|
|
|
xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
|
|
if ispc,
|
|
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
|
|
else
|
|
slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
|
|
end
|
|
|
|
startPos=slashPos(length(slashPos)-1) +1;
|
|
endPos=slashPos(length(slashPos)) -1
|
|
expStr= {xp(startPos:endPos)}
|
|
|
|
Exp(zoneSel).hOLname(traceN)= usrGnSp; %spotDescrip; %graphStr; %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
|
|
Exp(zoneSel).hOLexpNm(traceN)= expStr; %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
|
|
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
|
|
%Exp(zoneSel).hOLplateNum(traceN)= plateNum;
|
|
|
|
%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));
|
|
|
|
%if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end % Displays the value.
|
|
%if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
|
|
%if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
|
|
%if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end %graphStr);end % Displays the value.
|
|
%if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end %graphStr);end
|
|
%if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end %graphStr);end
|
|
catch
|
|
catchissue='Ln33 EZlstBoxCmpExt'
|
|
msg='Error'
|
|
end % trycatch zoneSel<4 datatip selection from Image (not from an OverLay Plot)
|
|
%**************Write Spot and Exp Info to OLay title areas****************************************************************************
|
|
|
|
if zoneSel==1, %&& get(ghandles.rotPB1,'value')~=1
|
|
if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay1,'FontSize',8);end
|
|
set(ghandles.OLay1,'string', Exp(zoneSel).hOLname(traceN));
|
|
if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp1,'FontSize',8);end
|
|
set(ghandles.OLexp1,'string',Exp(zoneSel).hOLexpNm(traceN));
|
|
end
|
|
if zoneSel==2 %&& get(ghandles.rotPB2,'value') ~=1
|
|
if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay2,'FontSize',8);end
|
|
set(ghandles.OLay2,'string', Exp(zoneSel).hOLname(traceN));
|
|
if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp2,'FontSize',8);end
|
|
set(ghandles.OLexp2,'string',Exp(zoneSel).hOLexpNm(traceN));
|
|
end
|
|
if zoneSel==3 %&& get(ghandles.rotPB3,'value') ~=1
|
|
if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay3,'FontSize',8);end
|
|
set(ghandles.OLay3,'string', Exp(OLay).hOLname(traceN));
|
|
if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp3,'FontSize',8);end
|
|
set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(traceN));
|
|
end
|
|
%}
|
|
%**********************************************************************
|
|
|
|
%{
|
|
%elseif RFcmpGFlg==1
|
|
K= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks= num2str(K);
|
|
r= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs= num2str(r);
|
|
l= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls= num2str(l);
|
|
Kl= K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
|
|
Ku= K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
|
|
rl= r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
|
|
ru= r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
|
|
lfast= l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
|
|
lslow= l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
|
|
end
|
|
%}
|
|
%Exp(expN).Dexp(n).UsrmdPindx= [];
|
|
%Exp(expN).Dexp(n).UsrmdPpltN= [];
|
|
%Exp(expN).Dexp(n).UsrmdPscanN= [];
|
|
%Exp(expN).Dexp(n).UsrMedianP= [];
|
|
%Exp(expN).Dexp(n).stdP= [];
|
|
%Exp(expN).Dexp(n).meanP= [];
|
|
%Exp(expN).Dexp(n).minP= [];
|
|
%Exp(expN).Dexp(n).maxP= [];
|
|
|
|
%Exp(expN).Dexp(n).RFmdGLB= {[]};
|
|
%Exp(expN).Dexp(n).RFmdGindx= [];
|
|
%Exp(expN).Dexp(n).RFmdGpltN= [];
|
|
%Exp(expN).Dexp(n).RFmdGscanN= [];
|
|
|
|
%UsrmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
|
|
%UsrmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
|
|
%UsrmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
|
|
%lstindx=lstindx+1;
|
|
%lstindxOrf= lstindxOrf+1;
|
|
%{
|
|
usrGLbl= strcat(usrGnSp,'UmdG('); %accomodate User Ref Selection
|
|
aa(lstindx,1)= strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
|
|
aa(lstindx,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
|
|
bb(lstindxOrf,1)= strcat(usrGLbl,num2str(d),')'); %remove string2cell brackets {...}
|
|
bb(lstindxOrf,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))}; %,'std_',num2str(std2))};
|
|
%Composite Reference Amalgum Plot ******************
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
aa(lstindx,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')');
|
|
aa(lstindx,2)={''};
|
|
bb(lstindxOrf,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')');
|
|
bb(lstindxOrf,2)={''};
|
|
%*****************************************************
|
|
%}
|
|
%{
|
|
lstindx=lstindx+1;
|
|
lstindxOrf= lstindxOrf+1;
|
|
usrPLbl= strcat(usrGnSp,'UmdP('); %accomodate User Ref Selection
|
|
aa(lstindx,1)= strcat(usrPLbl,num2str(d),')');
|
|
aa(lstindx,2)= {strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};
|
|
bb(lstindxOrf,1)= strcat(usrPLbl,num2str(d),')'); %remove string2cell brackets {...}
|
|
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};
|
|
|
|
Exp(expN).Dexp(n).UsrmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
|
|
Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))= medianIndxP;
|
|
Exp(expN).Dexp(n).UsrmdPpltN(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(n).UsrmdPscanN(d,dMPs(mm))=usrScNdisp;
|
|
Exp(expN).Dexp(n).UsrMedianP(d,dMPs(mm))= mval1Disp;
|
|
Exp(expN).Dexp(n).stdP(d,dMPs(mm))= std1Disp;
|
|
Exp(expN).Dexp(n).meanP(d,dMPs(mm))= mean1Disp;
|
|
Exp(expN).Dexp(n).minP(d,dMPs(mm))= minDisp;
|
|
Exp(expN).Dexp(n).maxP(d,dMPs(mm))= maxDisp;
|
|
|
|
Exp(expN).Dexp(n).UsrCmpPL.dm(d).med= mval1Disp; %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPL.dm(d).mean= mean1Disp; %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPL.dm(d).std= std1Disp; %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPL.dm(d).min= minDisp; %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPL.dm(d).max= maxDisp; %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPK.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
|
|
Exp(expN).Dexp(n).UsrCmpPK.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPK.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPK.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPK.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPr.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPr.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPr.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPr.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
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Exp(expN).Dexp(n).UsrCmpPr.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026
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%}
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%Exp(expN).Dexp(n).UsrmdGindx(d)= nzPosIndxDG;
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%Exp(expN).Dexp(n).UsrmdGpltN(d)= UsrmdDGloc(d,1);
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%Exp(expN).Dexp(n).UsrmdGscanN(d)= uu(nzPosIndxDG,4);
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%{
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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(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
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%Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroPindx;
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catch
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catchissue='try at Ln565'
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%Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
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%Exp(expN).Dexp(n).UsrmdPindx(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(n).UsrmdPpltN= dMPs(mm);
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catch
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catchissue='Ln619'
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%Exp(expN).Dexp(n).UsrmdPpltN= 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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%}
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