Add ezview
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299
workflow/apps/matlab/ezview/EZplotUcmp.m
Executable file
299
workflow/apps/matlab/ezview/EZplotUcmp.m
Executable file
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%EZplotUcmp.m
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%***********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 Single and Multi experiment 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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traceN=Exp(expN).traceN;
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DexpN= Exp(expN).DexpN;
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dmSel=Exp(zoneSel).Dexp(DexpN).pertSel;
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%dmSel= str2num(get(ghandles.DMed3,'string'))
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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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usrGene= selStrNm(1:(patrnN(1)-1));
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if strcmpi(selStrNm(1:3),'RF-')
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usrGeneSearch= selStrNm(4:(patrndash(2)-1));
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elseif strcmp(selStrNm(1:3),'RF1')
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usrGeneSearch= selStrNm(1:3);
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else
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usrGeneSearch= 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'), 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= DexpN:DexpN %n= 1:Exp(expN).DexpLength %LOOP Thru DayExps
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n= DexpN;
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MPnum=length(Exp(expN).Dexp(DexpN).MP);
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DMnum= length(Exp(expN).Dexp(DexpN).DM.drug);
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%Extract expDay from ExpName string
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dayNpos= max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
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dayLbl= Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
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%*********************************
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dRF1indx=0;
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usrSp= usrSpec; %user entry of Specifics for Ref selection
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%*******************************************************
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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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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(DexpN).MP(mp).genename{1}(ind384))==38991,
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Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)={'OCT1_'};
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elseif isnumeric(cell2mat(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)))
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Exp(expN).Dexp(DexpN).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(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
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strcmpi((Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384)),usrSp)))...
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|| ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
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strcmpi(usrSp,'None'))) ),
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dRF1indx=dRF1indx+1;
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Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),':',' ');
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drf(dRF1indx,1)= (Exp(expN).Dexp(DexpN).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(DexpN).MP(mp).specifics{1}(ind384));
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end %if isempty(regexpi(char((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384))),'blank'))...
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%*******************************************************************************
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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 %end associated with for mp=1:length(Exp(expN).Dexp(DexpN).MP)
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%*****************************************************
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%************************************************************************************************
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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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%************************************
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dMPs= unique(cell2mat(drf(:,2)));
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%*****************************************
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for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug)
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for mm=1:length(dMPs) % length(chgIndx)
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usrScNdisp=((dMPs(mm)-1)*DMnum)+(d);
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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(DexpN).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(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
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vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,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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%for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug)
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NZusrIndxG=[];
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NZusrIndxG= find(vvL);
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if isempty(nonzeros(vvL)), nonZeroCntD=0;
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else 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{d}= vvL(NZusrIndxG);
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UsrKvals{d}= vvK(NZusrIndxG);
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Usrrvals{d}= vvr(NZusrIndxG);
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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
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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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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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%#######################################################################
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%***********PLOT Values Selected Gene-Specifics Composite ******************************************try
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if NoGrowthflg==0
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smpSz= size(NZusrIndxG,1);
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K= median(cell2mat((UsrKvals(dmSel)))); Ks= num2str(K); Kstd= std(cell2mat((UsrKvals(dmSel)))); KstdStr= num2str(Kstd);
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r= median(cell2mat((Usrrvals(dmSel)))); rs= num2str(r); rstd= std(cell2mat((Usrrvals(dmSel)))); rstdStr= num2str(rstd);
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l= median(cell2mat((UsrLvals(dmSel)))); Ls= num2str(l); Lstd= std(cell2mat((UsrLvals(dmSel)))); LstdStr= num2str(Lstd);
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Kl= K - Kstd; %std(UsrKvals(dmSel));
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Ku= K + Kstd; %std(UsrKvals(dmSel));
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rl= r - rstd; %std(Usrrvals(dmSel));
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ru= r + rstd; %std(UsrKvals(dmSel));
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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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plateNum=(LBmp-1)*destPerMP + dmSel;
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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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Exp(expN).Trace(traceN).UsrGLB= usrGnSp;
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Exp(expN).Trace(traceN).dmSel= dmSel;
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Exp(expN).Trace(traceN).DexpN= DexpN;
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for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug) %LOOP Thru DrugMedias
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Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrLvals= UsrLvals(d);
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Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrKvals= UsrKvals(d);
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Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).Usrrvals= Usrrvals(d);
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end
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%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
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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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%************************************************************************
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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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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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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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Reference in New Issue
Block a user