252 lines
10 KiB
Matlab
Executable File
252 lines
10 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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global ghandles
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global Exp
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global exDlst
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global exFolder
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traceN=Exp(expN).traceN;
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DexpN=Exp(expN).DexpN; % Temp input for development
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patrnN=strfind(selGnOrf{1},':'); %Extract Gene-Orf Name
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patrndash=strfind(selGnOrf{1},'-');
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selStrNm=char(selGnOrf)
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if strcmpi(selStrNm(1:3),'RF-')
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usrGene=selStrNm(4:(patrndash(2)-1));
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else
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usrGene=selStrNm(1:(patrnN(1)-1));
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end
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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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usrSpec=cell2mat(answer(1));
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if strcmpi(usrSpec,'None')
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usrGnSp={strcat(usrGene,'-')};
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elseif length(usrSpec)> 8,
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trimUspec=usrSpec(1:8);
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usrGnSp=strcat(usrGene,',',{trimUspec});
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else
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trimUspec=usrSpec;
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usrGnSp=strcat(usrGene,',',{trimUspec});
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end
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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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%Extract expDay from ExpName string
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dayNpos=max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'))
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dayLbl=Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);
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dRF1indx=0;
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usrSp=usrSpec; %user entry of Specifics for Ref selection
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for mp=1:length(Exp(expN).Dexp(n).MP)
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for ind384=1:384
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try
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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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% 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)={mp}; drfMP(dRF1indx,mp)=mp;
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drf(dRF1indx,3)={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
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catch
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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
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vvL=[]; %Initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
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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,2))~=cell2mat(drf((j-1),2)), 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)=size(drf,1) +1; %length(drf)+1;
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vvL=zeros(size(drf,1),1 ); %length(drf)+1;
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dMPs=unique(cell2mat(drf(:,2)));
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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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NZusrIndx=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); medianIndxDisp=NZusrIndx;
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vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5);
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% For Global Ref Composite 17_1009
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vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
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vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4);
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end
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% Calc. Global Mean, Std, And Median For Distributed References
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for d=dmSel:dmSel
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NZusrIndxG=[];
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NZusrIndxG=find(vvL);
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if isempty(nonzeros(vvL))
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nonZeroCntD=0;
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else
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nonZeroCntD=length(nonzeros(vvL));
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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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NZusrIndxG=NZusrIndxG(:);
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if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
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UsrLvals{n}=vvL(NZusrIndxG);
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UsrKvals{n}=vvK(NZusrIndxG);
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Usrrvals{n}=vvr(NZusrIndxG);
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end
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end
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end
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end
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if ~exist('drf','var'),
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errordlg('Gene-Specifics combination not found. Check spelling of Specifics entry.','Entry Warning');
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break;
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end
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NoGrowthflg=0;
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if isempty(vvL),
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warndlg('No Growth condition found for Gene-Specifics combination. . ','No Growth warning');
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NoGrowthflg=1;
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end
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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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% Plot Values Selected Gene-Specifics Composite
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if NoGrowthflg==0
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smpSz=size(NZusrIndxG,1);
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K=median(cell2mat((UsrKvals(DexpN)))); Ks=num2str(K); Kstd=std(cell2mat((UsrKvals(DexpN)))); KstdStr=num2str(Kstd);
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r=median(cell2mat((Usrrvals(DexpN)))); rs=num2str(r); rstd=std(cell2mat((Usrrvals(DexpN)))); rstdStr=num2str(rstd);
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l=median(cell2mat((UsrLvals(DexpN)))); Ls=num2str(l); Lstd=std(cell2mat((UsrLvals(DexpN)))); LstdStr=num2str(Lstd);
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Kl=K - Kstd; %std(UsrKvals(DexpN));
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Ku=K + Kstd; %std(UsrKvals(DexpN));
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rl=r - rstd; %std(Usrrvals(DexpN));
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ru=r + rstd; %std(UsrKvals(DexpN));
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lfast=l - Lstd;
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lslow=l + Lstd;
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elseif NoGrowth==1 %if all data is zero (NoGrowth)
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smpSz=size(NZusrIndxG,1);
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K=0; Ks=num2str(K); Kstd=0; KstdStr=num2str(0);
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r=0; rs=num2str(r); rstd=0; rstdStr=num2str(0);
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l=0; Ls=num2str(l); Lstd=0; LstdStr=num2str(0);
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Kl=K - Kstd;
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Ku=K + Kstd;
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rl=r - rstd;
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ru=r + rstd;
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lfast=l - Lstd;
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lslow=l + Lstd;
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end
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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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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
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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
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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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Exp(expN).Trace(traceN).UsrGLB=usrGnSp;
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Exp(expN).Trace(traceN).dmSel=dmSel;
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for n=1:Exp(expN).DexpLength % Loop Thru DayExps
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Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrLvals=UsrLvals(n);
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Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrKvals=UsrKvals(n);
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Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).Usrrvals=Usrrvals(n);
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end
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% Store L R and K valves for manual selected 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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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
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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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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;
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Exp(zoneSel).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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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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msg='Error'
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end
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