bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Format DgenResults.m

Browse Source
This commit is contained in:
Bryan Roessler
2024-07-25 12:45:16 -04:00
parent adf507476d
commit 4d72a078b5
2 changed files with 560 additions and 613 deletions
Download Patch File Download Diff File Expand all files Collapse all files

403
workflow/templates/easy/DgenResults.m
View File

@@ -1,5 +1,5 @@
%% CALLED BY EASYconsole.m %% %% CALLED BY EASYconsole.m %%
%to 'Fotos' from 'PTmaps' % Updated 240724 Bryan C Roessler to improve file operations and portability
%Console globals******* %Console globals*******
global ExpPath global ExpPath
global resDir global resDir
@@ -8,83 +8,70 @@ global ImParMat
ln=1; ln=1;
%******Version compatability fixes*******assoc'd with diff and solve v11a='7.12.0.635 (R2011a)'; %******Version compatability fixes*******assoc'd with diff and solve v11a='7.12.0.635 (R2011a)';
if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3) if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4); fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
sols= solve(fd4); sols=solve(fd4);
else %accomodate new matlab changes after 2014a fix 2nd update 23_0227 else %accomodate new matlab changes after 2014a fix 2nd update 23_0227
syms t K r l; syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4); fd4=diff(K / (1 + exp(-r* (t - l ))),t,4);
sols= solve(fd4); sols=solve(fd4);
tmpswap= sols(1); tmpswap=sols(1);
sols(1)= sols(3); sols(1)=sols(3);
sols(3)= tmpswap; sols(3)=tmpswap;
end end
%MPnum=ImParMat(1); %MPnum=ImParMat(1);
%opt = questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both'); %opt=questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both');
opt='Res'; opt='Res';
if ~exist('ImParMat','var') || isempty(ImParMat) if ~exist('ImParMat','var') || isempty(ImParMat)
load ImParameters load ImParameters
end end
destPerMP=ImParMat(2); destPerMP=ImParMat(2);
load (ExpOutmat); load (ExpOutmat);
load (fullfile(ExpPath,'MasterPlateFiles','MPDMmat.mat')) load (fullfile(ExpPath,'MasterPlateFiles','MPDMmat.mat'))
numOfDrgs= length(DM.drug); numOfDrgs=length(DM.drug);
numOfMeds= length(DM.media); numOfMeds=length(DM.media);
destPerMP=numOfDrgs; destPerMP=numOfDrgs;
%Determine the longest set of intensity(tPts) for the Experiment Data Set %Determine the longest set of intensity(tPts) for the Experiment Data Set
maxNumIntens=0; maxNumIntens=0;
for n=1:size(scan,2) for n=1:size(scan,2)
for m=1:size(scan(n).plate,2) for m=1:size(scan(n).plate,2)
maxNumIntens= max(maxNumIntens,size(scan(n).plate(m).intens,2)); maxNumIntens=max(maxNumIntens,size(scan(n).plate(m).intens,2));
end end
end end
if length(ExpPath)== max(strfind(ExpPath,'\')) if length(ExpPath)==max(strfind(ExpPath,'\'))
localExpPath=ExpPath(1:end-1); localExpPath=ExpPath(1:end-1);
else else
localExpPath=ExpPath; localExpPath=ExpPath;
end end
if ispc %Linux accommodation if ispc %Linux accommodation
expNm=localExpPath(max(strfind(localExpPath,'\'))+1:end); expNm=localExpPath(max(strfind(localExpPath,'\'))+1:end);
else drivePos=min(strfind(localExpPath,'\'));
if isunix,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end elseif ((isunix) || (ismac))
if ismac,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end)
drivePos=min(strfind(localExpPath,'/'));
end end
if ispc
drivePos=min(strfind(localExpPath,'\'));
else
drivePos= min(strfind(localExpPath,'/'));
end
drive= localExpPath(1:(drivePos-1));
drive=localExpPath(1:(drivePos-1));
DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles'); DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
%DBupload=['G:\EZdbFiles\DBupLOADfiles']
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_Output.txt') %'\PrintResults\zDevelCFitOutIndxSelectedRawDatTimesDrugMedia.txt'
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_Output.txt') % Print !Dbase file in PrintResults dir
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_',expNm,'.txt')
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_',expNm,'.txt')
%Added to allow backward compatability************************************ %Added to allow backward compatability************************************
%Test for CFoutStd as indication of 2018version with r_refined fit code;If %Test for CFoutStd as indication of 2018version with r_refined fit code;If
%earlier version with only a standard composite fite, Print results to %earlier version with only a standard composite fite, Print results to
%!!ResultsStd_...txt only %!!ResultsStd_...txt only
%***********************
try try
scan(1).plate(1).CFoutStd(1,1); scan(1).plate(1).CFoutStd(1,1);
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsELr_',expNm,'.txt')); resultsFilename=fullfile(resDir,'PrintResults', strcat('!!ResultsELr_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseELr_',expNm,'.txt')); DBfilename=fullfile(resDir,'PrintResults', strcat('!!DbaseELr_',expNm,'.txt'));
catch catch
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt')); resultsFilename=fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt')); DBfilename=fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
end end
%**************************************************************************
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end if isequal(opt,'Res')||isequal(opt,'Both'),fid=fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header fprintf(fid,'%d\t',ln); %Results header
@@ -97,33 +84,40 @@ mpCnt=0;
totPlCnt=0; totPlCnt=0;
drgCnt=0; drgCnt=0;
medCnt=0; medCnt=0;
%load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
try try
load(fullfile(resDir,'Fotos','Nbdg')) %Convolute scan array data into plates load(fullfile(resDir,'Fotos','Nbdg')) %Convolute scan array data into plates
catch catch
load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
end end
for s=1:size(scan,2) for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo %Convolute scan array data into plates DconB for DBcombo
clear Diag clear Diag
try try
Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:); Diag(:,:,:,1)=sbdg{s}(1:1:24,16:-1:1,:);
catch catch
sbdg{s}; sbdg{s};
end end
%*****************************************************
for p=1:size((scan(s).plate),2) for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1; totPlCnt=totPlCnt+1;
if destPerMP>1 && rem(totPlCnt,destPerMP)==1
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end mpCnt=mpCnt+1
if destPerMP==1,mpCnt=mpCnt+1; end end
pertCnt= rem(totPlCnt,destPerMP); if destPerMP==1
if pertCnt==0, pertCnt= destPerMP;end mpCnt=mpCnt+1
pert= strcat('Perturb_',num2str(pertCnt)); end
s pertCnt=rem(totPlCnt,destPerMP);
p if pertCnt==0
pertCnt=destPerMP
end
pert=strcat('Perturb_',num2str(pertCnt));
s % TODO seems wrong
p % TODO seems wrong
clear outCmat clear outCmat
outCmat=scan(s).plate(p).CFout; outCmat=scan(s).plate(p).CFout;
%Print Time Point HEADER for each plate for newly added intensity data %Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\n'); fprintf(fid, '\n');
@@ -132,10 +126,10 @@ for s=1:size(scan,2)
fprintf(fid,'Scan\tPlate\tRow\tCol\t'); fprintf(fid,'Scan\tPlate\tRow\tCol\t');
try try
asd=cell2mat(scan(s).plate(1).CFparameters(1)); asd=cell2mat(scan(s).plate(1).CFparameters(1));
aucEndPt= strcat('AUC',num2str(asd(9))); aucEndPt=strcat('AUC',num2str(asd(9)));
catch catch
asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384)); asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
aucEndPt= strcat('AUC',num2str(asd(9))); aucEndPt=strcat('AUC',num2str(asd(9)));
end end
fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene'); fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
@@ -146,42 +140,35 @@ for s=1:size(scan,2)
fprintf(fid, '\ttc11Cut\ttc12Cut\ttc21Cut\ttc22Cut'); %'\tEarly1\tEarly2\tLate1\tLate2'); 17_0629 MinBaseIntens update for MedianBase label fprintf(fid, '\ttc11Cut\ttc12Cut\ttc21Cut\ttc22Cut'); %'\tEarly1\tEarly2\tLate1\tLate2'); 17_0629 MinBaseIntens update for MedianBase label
end end
fprintf(fid, '\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); fprintf(fid, '\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
end end
clear outTseries clear outTseries
outTseries=[]; outTseries=[];
outTseries=scan(s).plate(p).tSeries; outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1); TseriesSize=size(outTseries,1);
%***************************************************************
%clear outCmat
%outCmat=scan(s).plate(p).CFout;
clear outIntens clear outIntens
outIntens=[]; outIntens=[];
RawIntens=[]; RawIntens=[];
RawIntens=scan(s).plate(p).intens; RawIntens=scan(s).plate(p).intens;
RawIntensSize= size(RawIntens,2) RawIntensSize=size(RawIntens,2)
clear Ag; %Ag is Growth Area clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag; Ag=scan(s).plate(p).Ag;
AgSize= size(Ag); AgSize=size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize); dataLength=min(TseriesSize,RawIntensSize);
%for j=1:length(outTseries)%(size(outTseries,2)
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j)); fprintf(fid, '\t%.5f', outTseries(j));
end end
end end
%numBlkColTm=(maxNumIntens - size(outTseries,1));
numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1)); numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));
%for nn=1:numBlkColTm %extend to col beyond longest rawDataSet
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t'); fprintf(fid, '\t');
end end
fprintf(fid,'\tOrfRep'); fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics'); fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd'); fprintf(fid,'\tStrainBkGrd');
@@ -189,11 +176,10 @@ dataLength= min(TseriesSize,RawIntensSize);
ln=ln+1; ln=ln+1;
fprintf(fid,'%d\t',ln); fprintf(fid,'%d\t',ln);
end end
%*****************************************Begin Data Section
% Data
n=0; n=0;
for r=1:16 for r=1:16
for c=1:24 for c=1:24
n=n+1; n=n+1;
clear selcode; clear selcode;
@@ -201,54 +187,52 @@ dataLength= min(TseriesSize,RawIntensSize);
rSq=outCmat(n,6); rSq=outCmat(n,6);
lval=outCmat(n,5); lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030 if Kval<40, selcode=strcat(selcode,' K_Lo');end
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo');end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))... if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
||isnan(outCmat(n,10))||isnan(outCmat(n,11))... ||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN'); ||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end end
%*************RiseTime Calculation***************************************** % RiseTime Calculation
K= (outCmat(n,3)); K=(outCmat(n,3));
R= (outCmat(n,4)); R=(outCmat(n,4));
L= (outCmat(n,5)); L=(outCmat(n,5));
if R>0 && L>0 && K>0 if R>0 && L>0 && K>0
rr=R; ll=L; rr=R; ll=L;
tc1= eval(sols(2)); tc1=eval(sols(2));
tc2= eval(sols(3)); tc2=eval(sols(3));
LL= eval(sols(1)); LL=eval(sols(1));
riseTm= LL-tc1; riseTm=LL-tc1;
else else
riseTm=0; riseTm=0;
end end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030 if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end if outCmat(n,3)==0,selcode=strcat('0 ',selcode);end
orf=cell2mat(MP(mpCnt).orf{1}(n)); orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n)); gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n)); orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n)); specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n)); strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt}); drug=char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt}); conc=char(DM.conc{pertCnt});
media= char(DM.media{pertCnt}); media=char(DM.media{pertCnt});
try try
mod1= char(DM.mod1{pertCnt}); mod1=char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt}); conc1=char(DM.conc1{pertCnt});
catch catch
mod1= ' '; mod1=' ';
conc1= ' '; conc1=' ';
end end
try try
mod2= char(DM.mod2{pertCnt}); mod2=char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt}); conc2=char(DM.conc2{pertCnt});
catch catch
mod2= ' '; mod2=' ';
conc2= ' '; conc2=' ';
end end
if ~isempty(outCmat) if ~isempty(outCmat)
@@ -263,41 +247,37 @@ dataLength= min(TseriesSize,RawIntensSize);
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',... fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,17),outCmat(n,18),outCmat(n,19),... outCmat(n,17),outCmat(n,18),outCmat(n,19),...
outCmat(n,20),outCmat(n,21)); outCmat(n,20),outCmat(n,21));
%failPt= [s n r c]
%Added for data cut times used in 'r'optomized method 06/14/2018 % Added for data cut times used in 'r'optomized method 06/14/2018
if size(outCmat,2)==27 if (size(outCmat,2) == 27)
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f',... fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,24),outCmat(n,25),outCmat(n,26),outCmat(n,27)); outCmat(n,24),outCmat(n,25),outCmat(n,26),outCmat(n,27));
end end
fprintf(fid, '\t%d\t%d\t%d\t%d\t%d\t%d',... fprintf(fid, '\t%d\t%d\t%d\t%d\t%d\t%d',...
outCmat(n,22),outCmat(n,23),Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p)); outCmat(n,22),outCmat(n,23),Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print
%DBfile*******************************************
%riseTm calc*****
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end end
%**************** % DBfile
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq=0;dbKup=0; dbKlo=0; dbrup=0; dbrlo=0; dbLlo=0; dbLup=0;
if isnumeric(outCmat(n,6)), dbRsq=outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup=outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo=outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup=outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo=outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo=outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup=outCmat(n,12);end
end
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene); fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',... fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),... outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,... outCmat(n,5),dbRsq,dbKup,dbKlo,dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data % Add Intensities series to end of curve fit data
outIntens=[]; outIntens=[];
outIntens=zeros(384,dataLength); outIntens=zeros(384,dataLength);
intensBlob=''; intensBlob='';
@@ -305,34 +285,30 @@ dataLength= min(TseriesSize,RawIntensSize);
for j=1:dataLength %size(RawIntens,2) %size(outTseries,1) for j=1:dataLength %size(RawIntens,2) %size(outTseries,1)
if Ag(n)==0,Ag(n)=scan(s).Awindow;end if Ag(n)==0,Ag(n)=scan(s).Awindow;end
outIntens(n,j)= RawIntens(n,j)/Ag(n); outIntens(n,j)=RawIntens(n,j)/Ag(n);
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens
end end
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
if j<dataLength if j<dataLength
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';'); intensBlob=strcat(intensBlob,num2str(outIntens(n,j)),';');
else else
intensBlob= strcat(intensBlob,num2str(outIntens(n,j))); intensBlob=strcat(intensBlob,num2str(outIntens(n,j)));
end end
if outTseries(j)<.0001,outTseries(j)=0;end if outTseries(j)<.0001,outTseries(j)=0;end
if j<dataLength if j<dataLength
tmBlob= strcat(tmBlob,num2str(outTseries(j)),';'); tmBlob=strcat(tmBlob,num2str(outTseries(j)),';');
else else
tmBlob= strcat(tmBlob,num2str(outTseries(j))); tmBlob=strcat(tmBlob,num2str(outTseries(j)));
end
end
end end
end %if DB
end %j
%***************************
% Results
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t'); fprintf(fid, '\t');
end end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet % Masterplate sheet
if ~isnan(orfRep) if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep fprintf(fid, '\t%s', orfRep); %print OrfRep
@@ -349,19 +325,14 @@ dataLength= min(TseriesSize,RawIntensSize);
else else
fprintf(fid, '\t%s', ' '); fprintf(fid, '\t%s', ' ');
end end
%-----------------------------------------------
%****************************
fprintf(fid, '\n'); fprintf(fid, '\n');
ln=ln+1; ln=ln+1;
fprintf(fid,'%d\t',ln); fprintf(fid,'%d\t',ln);
end end
%****************************
%DB Raw Intensities and Timepoints %DB Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob ); fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet % Masterplate sheet
if ~isnan(orfRep) if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep ); fprintf(fid2, '\t%s',orfRep );
@@ -378,34 +349,30 @@ dataLength= min(TseriesSize,RawIntensSize);
else else
fprintf(fid2, '\t%s', ' '); fprintf(fid2, '\t%s', ' ');
end end
%---------------------------------
fprintf(fid2, '\n'); fprintf(fid2, '\n');
end %DB print end
end %if ~isempty(outCmat) end %if ~isempty(outCmat)
end %c end %c
end %r end %r
end %p end %p
end %s end %s
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid); fclose(fid);
end end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload) copyfile(DBfilename,DBupload)
catch ME catch ME
rep = getReport(ME, 'basic'); rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep); rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep) errordlg(rep)
end
end end
end %if DB
% ln; TODO removed by BCR, this doesn't seem necessary % ln; TODO removed by BCR, this doesn't seem necessary
%*********************************************************************** %***********************************************************************
%BEGIN PRINT RESULTS ROUTINE FOR STANDARD METHOD %BEGIN PRINT RESULTS ROUTINE FOR STANDARD METHOD
%*********************************************************************** %***********************************************************************
@@ -413,24 +380,24 @@ try
scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version
ln=1; ln=1;
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt')); resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt')); DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',localExpPath); fprintf(fid,'%s\t\n',localExpPath);
ln=ln+1; ln=ln+1;
fprintf(fid,'%d\t',ln); fprintf(fid,'%d\t',ln);
end end
mpCnt=0; mpCnt=0;
totPlCnt=0; totPlCnt=0;
drgCnt=0; drgCnt=0;
medCnt=0; medCnt=0;
for s=1:size(scan,2) for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo %Convolute scan array data into plates DconB for DBcombo
clear Diag clear Diag
try try
@@ -438,16 +405,15 @@ for s=1:size(scan,2)
catch catch
sbdg{s}; sbdg{s};
end end
%*****************************************************
for p=1:size((scan(s).plate),2) for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1; totPlCnt=totPlCnt+1;
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
if destPerMP==1,mpCnt=mpCnt+1; end if destPerMP==1,mpCnt=mpCnt+1; end
pertCnt= rem(totPlCnt,destPerMP); pertCnt= rem(totPlCnt,destPerMP);
if pertCnt==0, pertCnt= destPerMP;end if pertCnt==0, pertCnt= destPerMP;end
pert= strcat('Perturb_',num2str(pertCnt)); pert= strcat('Perturb_',num2str(pertCnt));
s s % BCR seems wrong
%Print Time Point HEADER for each plate for newly added intensity data %Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
@@ -471,8 +437,6 @@ for s=1:size(scan,2)
outTseries=[]; outTseries=[];
outTseries=scan(s).plate(p).tSeries; outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1); TseriesSize= size(outTseries,1);
%***************************************************************
clear outCmat clear outCmat
outCmat=scan(s).plate(p).CFoutStd; outCmat=scan(s).plate(p).CFoutStd;
clear outIntens clear outIntens
@@ -483,8 +447,8 @@ for s=1:size(scan,2)
clear Ag; %Ag is Growth Area clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag; Ag=scan(s).plate(p).Ag;
AgSize= size(Ag); AgSize= size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize); dataLength= min(TseriesSize,RawIntensSize);
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j)); fprintf(fid, '\t%.5f', outTseries(j));
@@ -497,7 +461,6 @@ dataLength= min(TseriesSize,RawIntensSize);
for nn=1:numBlkCol %extend to col beyond longest rawDataSet for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t'); fprintf(fid, '\t');
end end
fprintf(fid,'\tOrfRep'); fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics'); fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd'); fprintf(fid,'\tStrainBkGrd');
@@ -505,11 +468,10 @@ dataLength= min(TseriesSize,RawIntensSize);
ln=ln+1; ln=ln+1;
fprintf(fid,'%d\t',ln); fprintf(fid,'%d\t',ln);
end end
%*****************************************Begin Data Section
% Data
n=0; n=0;
for r=1:16 for r=1:16
for c=1:24 for c=1:24
n=n+1; n=n+1;
clear selcode; clear selcode;
@@ -525,46 +487,43 @@ dataLength= min(TseriesSize,RawIntensSize);
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN'); ||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end end
%*************RiseTime Calculation***************************************** % RiseTime Calculation
K= (outCmat(n,3)); K=(outCmat(n,3));
R= (outCmat(n,4)); R=(outCmat(n,4));
L= (outCmat(n,5)); L=(outCmat(n,5));
if R>0 && L>0 && K>0 if R>0 && L>0 && K>0
rr=R; ll=L; rr=R; ll=L;
tc1= eval(sols(2)); tc1=eval(sols(2));
tc2= eval(sols(3)); tc2=eval(sols(3));
LL= eval(sols(1)); LL=eval(sols(1));
riseTm= LL-tc1; riseTm= LL-tc1;
else else
riseTm=0; riseTm=0;
end end
%************************************************************************* if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n)); orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n)); gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n)); orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n)); specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n)); strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt}); drug=char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt}); conc=char(DM.conc{pertCnt});
media= char(DM.media{pertCnt}); media=char(DM.media{pertCnt});
try try
mod1= char(DM.mod1{pertCnt}); mod1=char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt}); conc1=char(DM.conc1{pertCnt});
catch catch
mod1= ' '; mod1=' ';
conc1= ' '; conc1=' ';
end end
try try
mod2= char(DM.mod2{pertCnt}); mod2=char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt}); conc2=char(DM.conc2{pertCnt});
catch catch
mod2= ' '; mod2=' ';
conc2= ' '; conc2=' ';
end end
if ~isempty(outCmat) if ~isempty(outCmat)
@@ -582,9 +541,10 @@ dataLength= min(TseriesSize,RawIntensSize);
fprintf(fid, '\t%d\t%d\t%d\t%d',... fprintf(fid, '\t%d\t%d\t%d\t%d',...
Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p)); Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print end
%DBfile*******************************************
%riseTm calc***** % DBFile
% RiseTime calculation
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0; dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
@@ -596,18 +556,16 @@ dataLength= min(TseriesSize,RawIntensSize);
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end end
%****************
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene); fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',... fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),... outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,... outCmat(n,5),dbRsq,dbKup,dbKlo,...
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f dbrup,dbrlo,dbLlo,dbLup);
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data % DB Analysis
% Add Intensities series to end of curve fit data
outIntens=[]; outIntens=[];
outIntens=zeros(384,dataLength); outIntens=zeros(384,dataLength);
intensBlob=''; intensBlob='';
@@ -631,19 +589,15 @@ dataLength= min(TseriesSize,RawIntensSize);
else else
tmBlob= strcat(tmBlob,num2str(outTseries(j))); tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end end
end %if DB end
end %j end
%***************************
% Results fprint
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t'); fprintf(fid, '\t');
end end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet % Masterplate sheet
if ~isnan(orfRep) if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep fprintf(fid, '\t%s', orfRep); %print OrfRep
@@ -660,19 +614,17 @@ dataLength= min(TseriesSize,RawIntensSize);
else else
fprintf(fid, '\t%s', ' '); fprintf(fid, '\t%s', ' ');
end end
%-----------------------------------------------
%****************************
fprintf(fid, '\n'); fprintf(fid, '\n');
ln=ln+1; ln=ln+1;
fprintf(fid,'%d\t',ln); fprintf(fid,'%d\t',ln);
end end
%****************************
%DB Raw Intensities and Timepoints
% Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both') if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob ); fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet % Masterplate sheet
if ~isnan(orfRep) if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep ); fprintf(fid2, '\t%s',orfRep );
@@ -689,37 +641,32 @@ dataLength= min(TseriesSize,RawIntensSize);
else else
fprintf(fid2, '\t%s', ' '); fprintf(fid2, '\t%s', ' ');
end end
%---------------------------------
fprintf(fid2, '\n'); fprintf(fid2, '\n');
end %DB print end %DB print
end %if ~isempty(outCmat) end %if ~isempty(outCmat)
end %c end %c
end %r end %r
end %p end %p
end %s end %s
if isequal(opt,'Res')||isequal(opt,'Both') if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid); fclose(fid);
end end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload) copyfile(DBfilename,DBupload)
catch ME catch ME
rep = getReport(ME, 'basic'); rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep); rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep) errordlg(rep)
end end
end %if DB end
ln;
catch msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])
catch ME
errorNstdResults='Catch at line720 for printing ResultsStd' errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version end
scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])

16
workflow/templates/easy/datatipp.m
View File

@@ -1,15 +1,15 @@
%% PART OF GUI FUNCTIONALITY %% %% PART OF GUI FUNCTIONALITY %%
function output_txt = datatipp(~,event_obj)
% Display the position of the data cursor % Display the position of the data cursor
function output_txt = datatipp(~,event_obj)
% obj Currently not used (empty) % obj Currently not used (empty)
% event_obj Handle to event object % event_obj Handle to event object
% output_txt Data cursor text string (string or cell array of strings). % output_txt Data cursor text string (string or cell array of strings).
pos=get(event_obj,'Position');
output_txt={['X: ',num2str(pos(1),4)],['Y: ',num2str(pos(2),4)]};
pos = get(event_obj,'Position'); % If there is a Z-coordinate in the position, display it as well
output_txt = {['X: ',num2str(pos(1),4)],... if length(pos) > 2
['Y: ',num2str(pos(2),4)]}; output_txt{end+1}=['Z: ',num2str(pos(3),4)];
end
% If there is a Z-coordinate in the position, display it as well
if length(pos) > 2
output_txt{end+1} = ['Z: ',num2str(pos(3),4)];
end end