% User find and build composite of Selected Gene Composite and % Plot it on OLay Plot and Trend plot DNLaxles % For Chonological Studies (multi Day Studies) % Called when Composite_ toggle button is clicked. % Data stored for printable Trend Plot production (click [L] in DNLaxes ) global ghandles global Exp global exDlst global exFolder traceN=Exp(expN).traceN; DexpN=Exp(expN).DexpN; % Temp input for development patrnN=strfind(selGnOrf{1},':'); %Extract Gene-Orf Name patrndash=strfind(selGnOrf{1},'-'); selStrNm=char(selGnOrf) if strcmpi(selStrNm(1:3),'RF-') usrGene=selStrNm(4:(patrndash(2)-1)); else usrGene=selStrNm(1:(patrnN(1)-1)); end prompt={'Enter Specifics Term if used to futher specify selection '} dlg_title='User Specifics Term for Refinement Composite'; num_lines=1; def={'None'}; answer=inputdlg(prompt,dlg_title,num_lines,def); usrSpec=cell2mat(answer(1)); if strcmpi(usrSpec,'None') usrGnSp={strcat(usrGene,'-')}; elseif length(usrSpec)> 8, trimUspec=usrSpec(1:8); usrGnSp=strcat(usrGene,',',{trimUspec}); else trimUspec=usrSpec; usrGnSp=strcat(usrGene,',',{trimUspec}); end for n=1:Exp(expN).DexpLength % LOOP Thru DayExps MPnum=length(Exp(expN).Dexp(n).MP); DMnum=length(Exp(expN).Dexp(n).DM.drug); %Extract expDay from ExpName string dayNpos=max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D')) dayLbl=Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end); dRF1indx=0; usrSp=usrSpec; %user entry of Specifics for Ref selection for mp=1:length(Exp(expN).Dexp(n).MP) for ind384=1:384 try % Insert test for numeric in genename and orf if isnumeric % Correct common EXCEL problem of converting OCT1 into a date numeric if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991, Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'}; elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))) Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '}; end % DISPersed REFerence capture and find Medians if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ... && strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp))) ... || ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) ... && strcmpi(usrSp,'None'))) ) dRF1indx=dRF1indx+1; Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' '); drf(dRF1indx,1)=(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)); drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)=mp; drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)=ind384; %drf(dRF1indx,7)=(Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)); end catch msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384)) end end % end associated with for ind384=1:384 mp end vvL=[]; %Initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0 if exist('drf','var') % Det. index of change from one MP to the next i=2; clear chgIndx chgIndx(1)=1; for j=1:length(drf(:,3)) if j>1 if cell2mat(drf(j,2))~=cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end end end chgIndx(length(chgIndx)+1)=size(drf,1) +1; %length(drf)+1; vvL=zeros(size(drf,1),1 ); %length(drf)+1; dMPs=unique(cell2mat(drf(:,2))); for mm=1:length(dMPs) % length(chgIndx) usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel); NZusrIndx=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp=NZusrIndx; vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5); % For Global Ref Composite 17_1009 vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3); vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4); end % Calc. Global Mean, Std, And Median For Distributed References for d=dmSel:dmSel NZusrIndxG=[]; NZusrIndxG=find(vvL); if isempty(nonzeros(vvL)) nonZeroCntD=0; else nonZeroCntD=length(nonzeros(vvL)); end % Calc. of median value for composite doesn't require and odd number of Indx items NZusrIndxG=NZusrIndxG(:); if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero UsrLvals{n}=vvL(NZusrIndxG); UsrKvals{n}=vvK(NZusrIndxG); Usrrvals{n}=vvr(NZusrIndxG); end end end end if ~exist('drf','var'), errordlg('Gene-Specifics combination not found. Check spelling of Specifics entry.','Entry Warning'); break; end NoGrowthflg=0; if isempty(vvL), warndlg('No Growth condition found for Gene-Specifics combination. . ','No Growth warning'); NoGrowthflg=1; end %Exp(expN).UgeneCnt=Exp(expN).UgeneCnt +1; %Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)=usrGnSp; % Plot Values Selected Gene-Specifics Composite if NoGrowthflg==0 smpSz=size(NZusrIndxG,1); K=median(cell2mat((UsrKvals(DexpN)))); Ks=num2str(K); Kstd=std(cell2mat((UsrKvals(DexpN)))); KstdStr=num2str(Kstd); r=median(cell2mat((Usrrvals(DexpN)))); rs=num2str(r); rstd=std(cell2mat((Usrrvals(DexpN)))); rstdStr=num2str(rstd); l=median(cell2mat((UsrLvals(DexpN)))); Ls=num2str(l); Lstd=std(cell2mat((UsrLvals(DexpN)))); LstdStr=num2str(Lstd); Kl=K - Kstd; %std(UsrKvals(DexpN)); Ku=K + Kstd; %std(UsrKvals(DexpN)); rl=r - rstd; %std(Usrrvals(DexpN)); ru=r + rstd; %std(UsrKvals(DexpN)); lfast=l - Lstd; lslow=l + Lstd; elseif NoGrowth==1 %if all data is zero (NoGrowth) smpSz=size(NZusrIndxG,1); K=0; Ks=num2str(K); Kstd=0; KstdStr=num2str(0); r=0; rs=num2str(r); rstd=0; rstdStr=num2str(0); l=0; Ls=num2str(l); Lstd=0; LstdStr=num2str(0); Kl=K - Kstd; Ku=K + Kstd; rl=r - rstd; ru=r + rstd; lfast=l - Lstd; lslow=l + Lstd; end 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 pertSel=Exp(zoneSel).Dexp(DexpN).pertSel; %floor(get(handles.DMsldr1,'value')); plateNum=(LBmp-1)*destPerMP + pertSel; MP=Exp(zoneSel).Dexp(DexpN).MP; try 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 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,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off'); Exp(expN).Trace(traceN).UsrGLB=usrGnSp; Exp(expN).Trace(traceN).dmSel=dmSel; for n=1:Exp(expN).DexpLength % Loop Thru DayExps Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrLvals=UsrLvals(n); Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrKvals=UsrKvals(n); Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).Usrrvals=Usrrvals(n); end % Store L R and K valves for manual selected Composite [C] plots Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K; Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast; 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]) catch catchissue='Ln100 EZlstBoxExt' end %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 gene=usrGnSp; orf='' %MP(1,LBmp).orf{1,1}(indx); geneOrfstr=strcat(gene,'_',orf,'_'); grfgenestr=strcat(gene,'_',orf,'_'); graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr); spotDescrip=strcat(graphStr,'->',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)=spotDescrip; Exp(zoneSel).hOLexpNm(traceN)=expStr; Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir}; Exp(zoneSel).hOLplateNum(traceN)=plateNum; 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 msg='Error' end