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

More EASYconsole work

Browse Source
This commit is contained in:
Bryan Roessler
2024-07-30 12:29:13 -04:00
parent 50914e93c7
commit fe9b338324
6 changed files with 263 additions and 243 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
workflow/apps/matlab/easy/DMPexcel2mat.m
View File

@@ -196,7 +196,6 @@ if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
sortedFiles=dmFiles{sortedIndices}; sortedFiles=dmFiles{sortedIndices};
drugMediaFile=sortedFiles{1}; drugMediaFile=sortedFiles{1};
fprintf('Using newest DrugMedia file: %s, skipping directory selection\n', drugMediaFile); fprintf('Using newest DrugMedia file: %s, skipping directory selection\n', drugMediaFile);
end end
catch Me catch Me
% This can be silent, not really an error % This can be silent, not really an error

10
workflow/apps/matlab/easy/EASYconsole.m
View File

@@ -65,10 +65,10 @@ function varargout = EASYconsole(varargin)
fprintf('WARNING: Running in standalone mode without PROJECT or PROJECT_SCANS_DIR environment variables (not recommended)\n'); fprintf('WARNING: Running in standalone mode without PROJECT or PROJECT_SCANS_DIR environment variables (not recommended)\n');
fprintf('Beginning parent scans directory search\n'); fprintf('Beginning parent scans directory search\n');
dirsToScan={ dirsToScan={
fullfile(parentDir, '..', '..', 'scans'), fullfile(parentDir, '..', '..', 'scans')
fullfile(parentDir, '..', '..', 'ExpJobs'), fullfile(parentDir, '..', '..', 'ExpJobs')
fullfile('mnt','data','scans'), fullfile('mnt','data','scans')
fullfile('mnt','data', 'ExpJobs'), fullfile('mnt','data', 'ExpJobs')
fullfile(parentDir, '..', '..', 'templates', 'scans-demo') fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
}; };
for i=1:length(dirsToScan) for i=1:length(dirsToScan)
@@ -78,7 +78,7 @@ function varargout = EASYconsole(varargin)
pattern='^\d{6}_.*_.*'; pattern='^\d{6}_.*_.*';
matchedDirs={dirs(regexp(subDirs.name, pattern)).name}; matchedDirs={dirs(regexp(subDirs.name, pattern)).name};
if ~isempty(matchedDirs) if ~isempty(matchedDirs)
fprintf('Found a non-empty scans directory in our list: %s\n', char(d); fprintf('Found a non-empty scans directory in our list: %s\n', char(d));
fprintf('Setting scansDir to %s\n', char(d)); fprintf('Setting scansDir to %s\n', char(d));
scansDir=fullfile(d); scansDir=fullfile(d);
end end

212
workflow/apps/matlab/ezview/EZinterAgingDev0.m
View File

@@ -6,7 +6,7 @@ function EZinterAgingDev0
AgMPDM=load(fullfile(scansDir,'MasterPlateFiles','MPDMmat.mat')); AgMPDM=load(fullfile(scansDir,'MasterPlateFiles','MPDMmat.mat'));
for i=1:size(openExpfile,2) for i=1:size(openExpfile,2)
ExpOutmat{i}= fullfile(scansDir,openExpfile{i}); ExpOutmat{i}=fullfile(scansDir,openExpfile{i});
EScan{i}=load(ExpOutmat{1}); EScan{i}=load(ExpOutmat{1});
end end
@@ -29,20 +29,20 @@ function EZinterAgingDev0
defaultanswer={'80','60','1','N','39','Y'}; defaultanswer={'80','60','1','N','39','Y'};
answer=inputdlg(prompt,name,numlines,defaultanswer); answer=inputdlg(prompt,name,numlines,defaultanswer);
negPercent= str2double(cell2mat(answer(1))); negPercent=str2double(cell2mat(answer(1)));
posPercent= str2double(cell2mat(answer(2))); posPercent=str2double(cell2mat(answer(2)));
DMstr= cell2mat(answer(3)); DMstr=cell2mat(answer(3));
DMcomas=strfind((cell2mat(answer(3))),','); DMcomas=strfind((cell2mat(answer(3))),',');
removInfinL= answer(4); removInfinL=answer(4);
numBins= str2double(cell2mat(answer(5))); numBins=str2double(cell2mat(answer(5)));
subplotX= answer(6); subplotX=answer(6);
% expN= str2double(cell2mat(answer(7))); % expN=str2double(cell2mat(answer(7)));
n=0; n=0;
for i= DMcomas, for i=DMcomas,
n=n+1 n=n+1
DMsel(n)= str2double(DMstr(i-1:i)) DMsel(n)=str2double(DMstr(i-1:i))
if i== max(DMcomas) if i==max(DMcomas)
DMsel(n+1)= str2double(DMstr(i:end)) DMsel(n+1)=str2double(DMstr(i:end))
end end
end end
@@ -57,46 +57,46 @@ function EZinterAgingDev0
for m=1:mpN for m=1:mpN
scnN=j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..; scnN=j + (dmN*(m-1)) % 1,6,11..; 2,7,12 ..; 3,8,13..;
Xn{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,5); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,5); Xn{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,5); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,5);
Xn{m,j,:}(Xn{m,j,:}==0)= 140; Xn{m,j,:}(Xn{m,j,:}==0)=140;
Xln{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,11); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,11); Xln{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,11); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,11);
Xhn{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,12); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,12); Xhn{m,j,:}=Exp(expN).scan(scnN).plate(1).CFout(:,12); % Exp(expN).scan(DM{j}(m)).plate(1).CFout(:,12);
intL{m,j,:} = (Xn{m,j,:} - Rn(j)); intL{m,j,:}=(Xn{m,j,:} - Rn(j));
intL{m,j,:}(Xn{m,j,:}==140)= 100; intL{m,j,:}(Xn{m,j,:}==140)=100;
intLhw{m,j,:} = ((Xn{m,1,:}-Xn{m,j,:}) - Rn(1)-Rn(j)); intLhw{m,j,:}=((Xn{m,1,:}-Xn{m,j,:}) - Rn(1)-Rn(j));
intLhw{m,j,:}(Xn{m,j,:}==140)= 100; intLhw{m,j,:}(Xn{m,j,:}==140)=100;
deltaXR{m,j}(Xn{m,j} >=(Rn(j)+Rs(j)))= ( Xln{m,j}(Xn{m,j} >=(Rn(j)+Rs(j))))- (Rn(j)+Rs(j)); deltaXR{m,j}(Xn{m,j} >=(Rn(j)+Rs(j)))=( Xln{m,j}(Xn{m,j} >=(Rn(j)+Rs(j))))- (Rn(j)+Rs(j));
deltaXR{m,j}(Xn{m,j} < (Rn(j)-Rs(j)))= ( Xhn{m,j}(Xn{m,j} < (Rn(j)-Rs(j))))- (Rn(j)-Rs(j)); deltaXR{m,j}(Xn{m,j} < (Rn(j)-Rs(j)))=( Xhn{m,j}(Xn{m,j} < (Rn(j)-Rs(j))))- (Rn(j)-Rs(j));
Xneg= Xhn{m,j}- (Rn(j)-Rs(j)); Xneg=Xhn{m,j}- (Rn(j)-Rs(j));
Xpos= Xln{m,j}- (Rn(j)+Rs(j)); Xpos=Xln{m,j}- (Rn(j)+Rs(j));
deltaXR{m,j}= zeros(1,384); deltaXR{m,j}=zeros(1,384);
for i=1:length(Xpos(:)), for i=1:length(Xpos(:))
% deltaXR{m,j}(i)= Xpos(i); % deltaXR{m,j}(i)=Xpos(i);
if deltaXR{m,j}(i)==0 if deltaXR{m,j}(i)==0
try try
if abs(Xpos(i))<abs(Xneg(i)), deltaXR{m,j}(i)= Xpos(i);end if abs(Xpos(i))<abs(Xneg(i)), deltaXR{m,j}(i)=Xpos(i);end
catch catch
end end
end end
end end
for i=1:length(Xneg(:)) for i=1:length(Xneg(:))
if deltaXR{m,j}(i)==0, deltaXR{m,j}(i)= Xneg(i); end if deltaXR{m,j}(i)==0, deltaXR{m,j}(i)=Xneg(i); end
try try
if abs(Xpos(i))>abs(Xneg(i)), deltaXR{m,j}(i)= Xneg(i); end if abs(Xpos(i))>abs(Xneg(i)), deltaXR{m,j}(i)=Xneg(i); end
catch catch
end end
end end
deltaXR{m,j,:}(Xln{m,j,:}==0)= 100; deltaXR{m,j,:}(Xln{m,j,:}==0)=100;
deltaXR{m,j,:}(isnan(Xln{m,j,:}))= 120; deltaXR{m,j,:}(isnan(Xln{m,j,:}))=120;
deltaXR{m,j,:}(Xhn{m,j,:}==0)= 100; deltaXR{m,j,:}(Xhn{m,j,:}==0)=100;
deltaXR{m,j,:}(isnan(Xhn{m,j,:}))= 120; deltaXR{m,j,:}(isnan(Xhn{m,j,:}))=120;
% Compile all gene related L values for the each pert-DM (j). % Compile all gene related L values for the each pert-DM (j).
addend=(1+((m-1)*384)) % ((((m-1)*j)*384)+1); addend=(1+((m-1)*384)) % ((((m-1)*j)*384)+1);
intLcmp(addend:addend+383,j)= cell2mat(intL(m,j,:)); % ((addend:addend+383),j)= cell2mat(intL(j,m,:)); intLcmp(addend:addend+383,j)=cell2mat(intL(m,j,:)); % ((addend:addend+383),j)=cell2mat(intL(j,m,:));
intLadjcmp(addend:addend+383,j)= cell2mat(deltaXR(m,j,:)); % ((addend:addend+383),j)= cell2mat(deltaXR(j,m,:)); intLadjcmp(addend:addend+383,j)=cell2mat(deltaXR(m,j,:)); % ((addend:addend+383),j)=cell2mat(deltaXR(j,m,:));
end end
% Remove RFs and Blank (or non annotated ' ') orf data Then % Remove RFs and Blank (or non annotated ' ') orf data Then
% Filter data per user intput % Filter data per user intput
@@ -120,13 +120,13 @@ function EZinterAgingDev0
centNegCnt=round(negPercent/100 * length(intLcmpSortLT0)); centNegCnt=round(negPercent/100 * length(intLcmpSortLT0));
intLposSel{j}=intLwoRFsorted{j}((length(intLcmpSortLT0)+centPosCnt): end,:); intLposSel{j}=intLwoRFsorted{j}((length(intLcmpSortLT0)+centPosCnt): end,:);
intLnegSel{j}=intLwoRFsorted{j}((1:(length(intLcmpSortLT0)-centNegCnt)),:); intLnegSel{j}=intLwoRFsorted{j}((1:(length(intLcmpSortLT0)-centNegCnt)),:);
posIntboundryCentralVal(j)= intLcmpSortGT0((centPosCnt),:); % For Histogram use posIntboundryCentralVal(j)=intLcmpSortGT0((centPosCnt),:); % For Histogram use
negIntboundryCentralVal(j)= intLcmpSortLT0(((length(intLcmpSortLT0))-(centNegCnt)),:); % For Histogram use negIntboundryCentralVal(j)=intLcmpSortLT0(((length(intLcmpSortLT0))-(centNegCnt)),:); % For Histogram use
% Find potential Interactors within selected range % Find potential Interactors within selected range
if j==DMsel(1) % Intc1, if j==DMsel(1) % Intc1,
InterslstPos{1}= intLposSel{DMsel(1)}(:,2) % intLcmpposInd{Intc1} InterslstPos{1}=intLposSel{DMsel(1)}(:,2) % intLcmpposInd{Intc1}
InterslstNeg{1}= intLnegSel{DMsel(1)}(:,2) % intLcmpnegInd{Intc1} InterslstNeg{1}=intLnegSel{DMsel(1)}(:,2) % intLcmpnegInd{Intc1}
elseif sum(ismember(DMsel,j))==1 %Intc1 && j<=IntcLst elseif sum(ismember(DMsel,j))==1 %Intc1 && j<=IntcLst
InterslstPos{1}=(intersect(InterslstPos{1},intLposSel{j}(:,2))); % ,intLcmpposInd{j})) InterslstPos{1}=(intersect(InterslstPos{1},intLposSel{j}(:,2))); % ,intLcmpposInd{j}))
InterslstNeg{1}=(intersect(InterslstNeg{1},intLnegSel{j}(:,2))); % ,intLcmpnegInd{j})) InterslstNeg{1}=(intersect(InterslstNeg{1},intLnegSel{j}(:,2))); % ,intLcmpnegInd{j}))
@@ -137,28 +137,28 @@ function EZinterAgingDev0
intLposDIndx{j}(:,2)=ceil((intLposSel{j}(:,2))/384); % mp plate numb column intLposDIndx{j}(:,2)=ceil((intLposSel{j}(:,2))/384); % mp plate numb column
intLposDIndx{j}(:,3)=(rem(intLposSel{j}(:,2),384)); intLposDIndx{j}(:,3)=(rem(intLposSel{j}(:,2),384));
nn=(intLposDIndx{j}(:,3)==0); nn=(intLposDIndx{j}(:,3)==0);
intLposDIndx{j}(nn,3)= 384; intLposDIndx{j}(nn,3)=384;
intLposDIndx{j}(:,1)= j + (dmN*((intLposDIndx{j}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3); intLposDIndx{j}(:,1)=j + (dmN*((intLposDIndx{j}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3);
intLnegDIndx{j}(:,2)=ceil((intLnegSel{j}(:,2))/384); % mp plate numb column intLnegDIndx{j}(:,2)=ceil((intLnegSel{j}(:,2))/384); % mp plate numb column
intLnegDIndx{j}(:,3)=(rem(intLnegSel{j}(:,2),384)); intLnegDIndx{j}(:,3)=(rem(intLnegSel{j}(:,2),384));
nn=(intLposDIndx{j}(:,3)==0); nn=(intLposDIndx{j}(:,3)==0);
intLnegDIndx{j}(nn,3)= 384; intLnegDIndx{j}(nn,3)=384;
intLnegDIndx{j}(:,1)= j + (dmN*((intLnegDIndx{j}(:,2))-1)); % scan numb intLnegDIndx{j}(:,1)=j + (dmN*((intLnegDIndx{j}(:,2))-1)); % scan numb
% ADJUSTED L for Reference Standard deviation(More conservative) Interaction List compilation % ADJUSTED L for Reference Standard deviation(More conservative) Interaction List compilation
intLadjwoRFs{j}(1,:)=intLadjcmp(Exp(expN).mutSpotIndx.woRFs,j); intLadjwoRFs{j}(1,:)=intLadjcmp(Exp(expN).mutSpotIndx.woRFs,j);
intLadjwoRFs{j}(2,:)= Exp(expN).mutSpotIndx.woRFs; % intLadjcmp(385:(mpN-1)*384,j); %intLadjcmp(Exp(expN).mutSpotIndx.woRFs,j); intLadjwoRFs{j}(2,:)=Exp(expN).mutSpotIndx.woRFs; % intLadjcmp(385:(mpN-1)*384,j); %intLadjcmp(Exp(expN).mutSpotIndx.woRFs,j);
if strcmpi(removInfinL,'Y') if strcmpi(removInfinL,'Y')
intLadjwoRFs0{j}(1,:)= intLadjwoRFs{j}(1,(intLadjwoRFs{j}(1,:)~= 100)) ; %intLcmp(Exp(1).mutSpotIndx.woRFs,j); intLadjwoRFs0{j}(1,:)=intLadjwoRFs{j}(1,(intLadjwoRFs{j}(1,:)~=100)) ; %intLcmp(Exp(1).mutSpotIndx.woRFs,j);
intLadjwoRFs0{j}(2,:)= intLadjwoRFs{j}(2,(intLadjwoRFs{j}(1,:)~= 100)) ; % Remove Index where spots are infinite (=100); intLadjwoRFs0{j}(2,:)=intLadjwoRFs{j}(2,(intLadjwoRFs{j}(1,:)~=100)) ; % Remove Index where spots are infinite (=100);
clear intLadjwoRFs clear intLadjwoRFs
intLadjwoRFs{j}(1,:)= intLadjwoRFs0{j}(1,:); intLadjwoRFs{j}(1,:)=intLadjwoRFs0{j}(1,:);
intLadjwoRFs{j}(2,:)= intLadjwoRFs0{j}(2,:); intLadjwoRFs{j}(2,:)=intLadjwoRFs0{j}(2,:);
end end
intLwoRFsortedAdj{j}= sortrows(intLadjwoRFs{j}',1); intLwoRFsortedAdj{j}=sortrows(intLadjwoRFs{j}',1);
clear intLadjSortGT0 intLadjSortLT0 clear intLadjSortGT0 intLadjSortLT0
tempIntLadj=intLwoRFsortedAdj{j}(:,1); tempIntLadj=intLwoRFsortedAdj{j}(:,1);
intLadjSortGT0=tempIntLadj((tempIntLadj) >=0); intLadjSortGT0=tempIntLadj((tempIntLadj) >=0);
@@ -171,8 +171,8 @@ function EZinterAgingDev0
negIntboundryCentralValAdj(j)=intLadjSortLT0(((length(intLadjSortLT0))-(centNegCntAdj)),:); negIntboundryCentralValAdj(j)=intLadjSortLT0(((length(intLadjSortLT0))-(centNegCntAdj)),:);
if j==DMsel(1) % Intc1 if j==DMsel(1) % Intc1
InterslstPosAdj{1}= intLposSelAdj{DMsel(1)}(:,2) % intLcmpposInd{Intc1} InterslstPosAdj{1}=intLposSelAdj{DMsel(1)}(:,2) % intLcmpposInd{Intc1}
InterslstNegAdj{1}= intLnegSelAdj{DMsel(1)}(:,2) % intLcmpnegInd{Intc1} InterslstNegAdj{1}=intLnegSelAdj{DMsel(1)}(:,2) % intLcmpnegInd{Intc1}
elseif sum(ismember(DMsel,j))==1 % j>Intc1 && j<=IntcLst elseif sum(ismember(DMsel,j))==1 % j>Intc1 && j<=IntcLst
InterslstPosAdj{1}=(intersect(InterslstPosAdj{1},intLposSelAdj{j}(:,2))); % ,intLcmpposInd{j})) InterslstPosAdj{1}=(intersect(InterslstPosAdj{1},intLposSelAdj{j}(:,2))); % ,intLcmpposInd{j}))
InterslstNegAdj{1}=(intersect(InterslstNegAdj{1},intLnegSelAdj{j}(:,2))); % ,intLcmpnegInd{j})) InterslstNegAdj{1}=(intersect(InterslstNegAdj{1},intLnegSelAdj{j}(:,2))); % ,intLcmpnegInd{j}))
@@ -183,14 +183,14 @@ function EZinterAgingDev0
intLposDIndxAdj{j}(:,2)=ceil((intLposSelAdj{j}(:,2))/384); % mp plate numb column intLposDIndxAdj{j}(:,2)=ceil((intLposSelAdj{j}(:,2))/384); % mp plate numb column
intLposDIndxAdj{j}(:,3)=(rem(intLposSelAdj{j}(:,2),384)); intLposDIndxAdj{j}(:,3)=(rem(intLposSelAdj{j}(:,2),384));
nn=(intLposDIndxAdj{j}(:,3)==0); nn=(intLposDIndxAdj{j}(:,3)==0);
intLposDIndx{j}(nn,3)= 384; intLposDIndx{j}(nn,3)=384;
intLposDIndxAdj{j}(:,1)= j + (dmN*((intLposDIndxAdj{j}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3); intLposDIndxAdj{j}(:,1)=j + (dmN*((intLposDIndxAdj{j}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3);
intLnegDIndxAdj{j}(:,2)=ceil((intLnegSelAdj{j}(:,2))/384); % mp plate numb column intLnegDIndxAdj{j}(:,2)=ceil((intLnegSelAdj{j}(:,2))/384); % mp plate numb column
intLnegDIndxAdj{j}(:,3)=(rem(intLnegSelAdj{j}(:,2),384)); intLnegDIndxAdj{j}(:,3)=(rem(intLnegSelAdj{j}(:,2),384));
nn=(intLposDIndxAdj{j}(:,3)==0); nn=(intLposDIndxAdj{j}(:,3)==0);
intLnegDIndxAdj{j}(nn,3)= 384; intLnegDIndxAdj{j}(nn,3)=384;
intLnegDIndxAdj{j}(:,1)= j + (dmN*((intLnegDIndxAdj{j}(:,2))-1)); % scan numb intLnegDIndxAdj{j}(:,1)=j + (dmN*((intLnegDIndxAdj{j}(:,2))-1)); % scan numb
end end
% Get interaction values for each DM drugmedia agar type % Get interaction values for each DM drugmedia agar type
@@ -199,56 +199,56 @@ function EZinterAgingDev0
IntersValsPosAdj=intLadjcmp(InterslstPosAdj{1},DMsel); IntersValsPosAdj=intLadjcmp(InterslstPosAdj{1},DMsel);
IntersValsNegAdj=intLadjcmp(InterslstNegAdj{1},DMsel); IntersValsNegAdj=intLadjcmp(InterslstNegAdj{1},DMsel);
%Build 'genelist' data sheet for interactors % Build 'genelist' data sheet for interactors
selIntPx{1}(:,6)=InterslstPos{1}; selIntPx{1}(:,6)=InterslstPos{1};
selIntPx{1}(:,2)=ceil((InterslstPos{1})/384); % mp plate numb column selIntPx{1}(:,2)=ceil((InterslstPos{1})/384); % mp plate numb column
selIntPx{1}(:,3)=(rem(InterslstPos{1},384)); selIntPx{1}(:,3)=(rem(InterslstPos{1},384));
nn=(selIntPx{1}(:,3)==0); nn=(selIntPx{1}(:,3)==0);
selIntPx{1}(nn,3)= 384; selIntPx{1}(nn,3)=384;
selIntPx{1}(:,4)= ceil(selIntPx{1}(:,3)/24); % row numb selIntPx{1}(:,4)=ceil(selIntPx{1}(:,3)/24); % row numb
selIntPx{1}(:,5)= rem(selIntPx{1}(:,3),24); selIntPx{1}(:,5)=rem(selIntPx{1}(:,3),24);
mm=(selIntPx{1}(:,5)==0); mm=(selIntPx{1}(:,5)==0);
selIntPx{1}(mm,5)= 24; selIntPx{1}(mm,5)=24;
selIntPx{1}(:,1)= j + (dmN*((selIntPx{1}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3); selIntPx{1}(:,1)=j + (dmN*((selIntPx{1}(:,2))-1)); % scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3);
selIntP= cell2mat(selIntPx); selIntP=cell2mat(selIntPx);
selIntNx{1}(:,6)=InterslstNeg{1}; selIntNx{1}(:,6)=InterslstNeg{1};
selIntNx{1}(:,2)=ceil((InterslstNeg{1})/384); % mp plate numb column selIntNx{1}(:,2)=ceil((InterslstNeg{1})/384); % mp plate numb column
selIntNx{1}(:,3)=(rem(InterslstNeg{1},384)); selIntNx{1}(:,3)=(rem(InterslstNeg{1},384));
nn=(selIntNx{1}(:,3)==0); nn=(selIntNx{1}(:,3)==0);
selIntNx{1}(nn,3)= 384; selIntNx{1}(nn,3)=384;
selIntNx{1}(:,4)= ceil(selIntNx{1}(:,3)/24); % row numb selIntNx{1}(:,4)=ceil(selIntNx{1}(:,3)/24); % row numb
selIntNx{1}(:,5)= rem(selIntNx{1}(:,3),24); selIntNx{1}(:,5)=rem(selIntNx{1}(:,3),24);
mm=(selIntNx{1}(:,5)==0); mm=(selIntNx{1}(:,5)==0);
selIntNx{1}(mm,5)= 24; selIntNx{1}(mm,5)=24;
selIntNx{1}(:,1)= j + (dmN*((selIntNx{1}(:,2))-1)); % scan numb selIntNx{1}(:,1)=j + (dmN*((selIntNx{1}(:,2))-1)); % scan numb
selIntN= cell2mat(selIntNx); selIntN=cell2mat(selIntNx);
for i=1:size(selIntP,1) for i=1:size(selIntP,1)
IPgene(i)=Exp(expN).MP(selIntP(i,2)).genename{1}(selIntP(i,3)); IPgene(i)=Exp(expN).MP(selIntP(i,2)).genename{1}(selIntP(i,3));
IPorf(i)= Exp(expN).MP(selIntP(i,2)).orf{1}(selIntP(i,3)); IPorf(i)=Exp(expN).MP(selIntP(i,2)).orf{1}(selIntP(i,3));
IPstrain(i)= Exp(expN).MP(selIntP(i,2)).strain{1}(selIntP(i,3)); IPstrain(i)=Exp(expN).MP(selIntP(i,2)).strain{1}(selIntP(i,3));
IPspecifics(i)=Exp(expN).MP(selIntP(i,2)).specifics{1}(selIntP(i,3)); IPspecifics(i)=Exp(expN).MP(selIntP(i,2)).specifics{1}(selIntP(i,3));
IPorfRep(i)=Exp(expN).MP(selIntP(i,2)).orfRep{1}(selIntP(i,3)); IPorfRep(i)=Exp(expN).MP(selIntP(i,2)).orfRep{1}(selIntP(i,3));
% Bad this is the L data for only the last selected DM perturbation % Bad this is the L data for only the last selected DM perturbation
% Would need to calculate each scan# for each DMsel value % Would need to calculate each scan# for each DMsel value
ipL(i)= Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),5); ipL(i)=Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),5);
ipLlower(i)= Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),11); ipLlower(i)=Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),11);
ipLupper(i)= Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),12); ipLupper(i)=Exp(expN).scan(selIntP(i,1)).plate(1).CFout(selIntP(i,3),12);
end end
for i=1:size(selIntN,1) for i=1:size(selIntN,1)
INgene(i)=Exp(expN).MP(selIntN(i,2)).genename{1}(selIntN(i,3)); INgene(i)=Exp(expN).MP(selIntN(i,2)).genename{1}(selIntN(i,3));
INorf(i)= Exp(expN).MP(selIntN(i,2)).orf{1}(selIntN(i,3)); INorf(i)=Exp(expN).MP(selIntN(i,2)).orf{1}(selIntN(i,3));
INstrain(i)= Exp(expN).MP(selIntN(i,2)).strain{1}(selIntN(i,3)); INstrain(i)=Exp(expN).MP(selIntN(i,2)).strain{1}(selIntN(i,3));
INspecifics(i)=Exp(expN).MP(selIntN(i,2)).specifics{1}(selIntN(i,3)); INspecifics(i)=Exp(expN).MP(selIntN(i,2)).specifics{1}(selIntN(i,3));
INorfRep(i)=Exp(expN).MP(selIntN(i,2)).orfRep{1}(selIntN(i,3)); INorfRep(i)=Exp(expN).MP(selIntN(i,2)).orfRep{1}(selIntN(i,3));
% Bad this is the L data for only the last selected DM perturbation % Bad this is the L data for only the last selected DM perturbation
% Would need to calculate each scan# for each DMsel value % Would need to calculate each scan# for each DMsel value
inL(i)= Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),5); inL(i)=Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),5);
inLlower(i)= Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),11); inLlower(i)=Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),11);
inLupper(i)= Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),12); inLupper(i)=Exp(expN).scan(selIntN(i,1)).plate(1).CFout(selIntN(i,3),12);
end end
% ADJUSTED with STD and curve fit boundaries to produce more conservative interaction values % ADJUSTED with STD and curve fit boundaries to produce more conservative interaction values
@@ -256,48 +256,48 @@ function EZinterAgingDev0
selIntPxAdj{1}(:,2)=ceil((InterslstPosAdj{1})/384); %mp plate numb column selIntPxAdj{1}(:,2)=ceil((InterslstPosAdj{1})/384); %mp plate numb column
selIntPxAdj{1}(:,3)=(rem(InterslstPosAdj{1},384)); selIntPxAdj{1}(:,3)=(rem(InterslstPosAdj{1},384));
nn=(selIntPxAdj{1}(:,3)==0); nn=(selIntPxAdj{1}(:,3)==0);
selIntPxAdj{1}(nn,3)= 384; selIntPxAdj{1}(nn,3)=384;
selIntPxAdj{1}(:,4)= ceil(selIntPxAdj{1}(:,3)/24); %row numb selIntPxAdj{1}(:,4)=ceil(selIntPxAdj{1}(:,3)/24); %row numb
selIntPxAdj{1}(:,5)= rem(selIntPxAdj{1}(:,3),24); selIntPxAdj{1}(:,5)=rem(selIntPxAdj{1}(:,3),24);
mm=(selIntPxAdj{1}(:,5)==0); mm=(selIntPxAdj{1}(:,5)==0);
selIntPxAdj{1}(mm,5)= 24; selIntPxAdj{1}(mm,5)=24;
selIntPxAdj{1}(:,1)= j + (dmN*((selIntPxAdj{1}(:,2))-1)); %scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3); selIntPxAdj{1}(:,1)=j + (dmN*((selIntPxAdj{1}(:,2))-1)); %scan numb column %intLposDIndx(:,2)* intLposDIndx(:,3);
selIntPAdj= cell2mat(selIntPxAdj); selIntPAdj=cell2mat(selIntPxAdj);
selIntNxAdj{1}(:,2)=ceil((InterslstNegAdj{1})/384); %mp plate numb column selIntNxAdj{1}(:,2)=ceil((InterslstNegAdj{1})/384); %mp plate numb column
selIntNxAdj{1}(:,3)=(rem(InterslstNegAdj{1},384)); selIntNxAdj{1}(:,3)=(rem(InterslstNegAdj{1},384));
nn=(selIntNxAdj{1}(:,3)==0); nn=(selIntNxAdj{1}(:,3)==0);
selIntNxAdj{1}(nn,3)= 384; selIntNxAdj{1}(nn,3)=384;
selIntNxAdj{1}(:,4)= ceil(selIntNxAdj{1}(:,3)/24); %row numb selIntNxAdj{1}(:,4)=ceil(selIntNxAdj{1}(:,3)/24); %row numb
selIntNxAdj{1}(:,5)= rem(selIntNxAdj{1}(:,3),24); selIntNxAdj{1}(:,5)=rem(selIntNxAdj{1}(:,3),24);
mm=(selIntNxAdj{1}(:,5)==0); mm=(selIntNxAdj{1}(:,5)==0);
selIntNxAdj{1}(mm,5)= 24; selIntNxAdj{1}(mm,5)=24;
selIntNxAdj{1}(:,1)= j + (dmN*((selIntNxAdj{1}(:,2))-1)); %scan numb selIntNxAdj{1}(:,1)=j + (dmN*((selIntNxAdj{1}(:,2))-1)); %scan numb
selIntNAdj= cell2mat(selIntNxAdj); selIntNAdj=cell2mat(selIntNxAdj);
for i=1:size(selIntPAdj,1) for i=1:size(selIntPAdj,1)
IPgeneAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).genename{1}(selIntPAdj(i,3)); IPgeneAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).genename{1}(selIntPAdj(i,3));
IPorfAdj(i)= Exp(expN).MP(selIntPAdj(i,2)).orf{1}(selIntPAdj(i,3)); IPorfAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).orf{1}(selIntPAdj(i,3));
IPstrainAdj(i)= Exp(expN).MP(selIntPAdj(i,2)).strain{1}(selIntPAdj(i,3)); IPstrainAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).strain{1}(selIntPAdj(i,3));
IPspecificsAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).specifics{1}(selIntPAdj(i,3)); IPspecificsAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).specifics{1}(selIntPAdj(i,3));
IPorfRepAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).orfRep{1}(selIntPAdj(i,3)); IPorfRepAdj(i)=Exp(expN).MP(selIntPAdj(i,2)).orfRep{1}(selIntPAdj(i,3));
% Bad this is the L data for only the last selected DM perturbation % Bad this is the L data for only the last selected DM perturbation
% Would need to calculate each scan# for each DMsel value % Would need to calculate each scan# for each DMsel value
ipLAdj(i)= Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),5); ipLAdj(i)=Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),5);
ipLlowerAdj(i)= Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),11); ipLlowerAdj(i)=Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),11);
ipLupperAdj(i)= Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),12); ipLupperAdj(i)=Exp(expN).scan(selIntPAdj(i,1)).plate(1).CFout(selIntPAdj(i,3),12);
end end
for i=1:size(selIntNAdj,1) for i=1:size(selIntNAdj,1)
INgeneAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).genename{1}(selIntNAdj(i,3)); INgeneAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).genename{1}(selIntNAdj(i,3));
INorfAdj(i)= Exp(expN).MP(selIntNAdj(i,2)).orf{1}(selIntNAdj(i,3)); INorfAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).orf{1}(selIntNAdj(i,3));
INstrainAdj(i)= Exp(expN).MP(selIntNAdj(i,2)).strain{1}(selIntNAdj(i,3)); INstrainAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).strain{1}(selIntNAdj(i,3));
INspecificsAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).specifics{1}(selIntNAdj(i,3)); INspecificsAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).specifics{1}(selIntNAdj(i,3));
INorfRepAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).orfRep{1}(selIntNAdj(i,3)); INorfRepAdj(i)=Exp(expN).MP(selIntNAdj(i,2)).orfRep{1}(selIntNAdj(i,3));
%Bad this is the L data for only the last selected DM perturbation %Bad this is the L data for only the last selected DM perturbation
%Would need to calculate each scan# for each DMsel value %Would need to calculate each scan# for each DMsel value
inLAdj(i)= Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),5); inLAdj(i)=Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),5);
inLlowerAdj(i)= Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),11); inLlowerAdj(i)=Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),11);
inLupperAdj(i)= Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),12); inLupperAdj(i)=Exp(expN).scan(selIntNAdj(i,1)).plate(1).CFout(selIntNAdj(i,3),12);
end end
@@ -306,11 +306,11 @@ function EZinterAgingDev0
figure figure
if strcmpi(subplotX,'Y') if strcmpi(subplotX,'Y')
for j=1:dmN for j=1:dmN
histLdata= intLwoRFsorted{j}(:,1); % intLcmp(385:(mpN-1)*384,j); histLdata=intLwoRFsorted{j}(:,1); % intLcmp(385:(mpN-1)*384,j);
% histLadjData=intLadjcmp(385:(mpN-1)*384,j); % histLadjData=intLadjcmp(385:(mpN-1)*384,j);
hgLdat{j}=histfitJR(histLdata,numBins,'kernel'); hgLdat{j}=histfitJR(histLdata,numBins,'kernel');
x{j}= get(hgLdat{j}(2),'xdata'); x{j}=get(hgLdat{j}(2),'xdata');
y{j}= get(hgLdat{j}(2),'ydata'); y{j}=get(hgLdat{j}(2),'ydata');
xb{j}=get(hgLdat{j}(1),'xdata'); xb{j}=get(hgLdat{j}(1),'xdata');
yb{j}=get(hgLdat{j}(1),'ydata'); yb{j}=get(hgLdat{j}(1),'ydata');
ybpostot{j}=sum(yb{j}(2,(xb{j}(1,:)>=0))); ybpostot{j}=sum(yb{j}(2,(xb{j}(1,:)>=0)));
@@ -329,20 +329,20 @@ function EZinterAgingDev0
hold off hold off
end end
scnsize=get(0,'screensize') scnsize=get(0,'screensize')
pos1= [round(scnsize(3)/40), round(scnsize(4)/2 +(scnsize(3)/80)),... pos1=[round(scnsize(3)/40), round(scnsize(4)/2 +(scnsize(3)/80)),...
round(scnsize(3) -round(scnsize(3)/80)),round(scnsize(4)/2 -round(scnsize(4)/80))] round(scnsize(3) -round(scnsize(3)/80)),round(scnsize(4)/2 -round(scnsize(4)/80))]
set(gcf,'outerposition',pos1) set(gcf,'outerposition',pos1)
set(gcf,'Name', 'Interaction Values '); set(gcf,'Name', 'Interaction Values ');
figure figure
for j=1:dmN for j=1:dmN
histLadjData= intLwoRFsortedAdj{j}(:,1); %intLadjcmp(385:(mpN-1)*384,j); histLadjData=intLwoRFsortedAdj{j}(:,1); %intLadjcmp(385:(mpN-1)*384,j);
hgLadj{j}=subplot(2, 4, j),histfitJR(histLadjData,numBins,'kernel') ; hold %hgLadj{j}=histfit(intLadjcmp(:,j),31,'kernel') hgLadj{j}=subplot(2, 4, j),histfitJR(histLadjData,numBins,'kernel') ; hold %hgLadj{j}=histfit(intLadjcmp(:,j),31,'kernel')
subplot(2, 4, j),plot(posIntboundryCentralValAdj(j), 1:3000,'--r') subplot(2, 4, j),plot(posIntboundryCentralValAdj(j), 1:3000,'--r')
subplot(2, 4, j),plot(negIntboundryCentralValAdj(j), 1:3000,'--g') subplot(2, 4, j),plot(negIntboundryCentralValAdj(j), 1:3000,'--g')
hold off hold off
end end
pos2= [round(scnsize(3)/40), round(scnsize(4)/30),... pos2=[round(scnsize(3)/40), round(scnsize(4)/30),...
round(scnsize(3) -scnsize(3)/80),round(scnsize(4)/2 -scnsize(4)/80)] round(scnsize(3) -scnsize(3)/80),round(scnsize(4)/2 -scnsize(4)/80)]
set(gcf,'outerposition',pos2) set(gcf,'outerposition',pos2)
set(gcf,'Name', 'Interaction Compensated by Standard Deviation and Upper/Lower Curvefit boundaries') set(gcf,'Name', 'Interaction Compensated by Standard Deviation and Upper/Lower Curvefit boundaries')
@@ -360,8 +360,8 @@ function EZinterAgingDev0
plot(posIntboundryCentralValAdj(j), 1:3000,'--r') plot(posIntboundryCentralValAdj(j), 1:3000,'--r')
plot(negIntboundryCentralValAdj(j), 1:3000,'--g') plot(negIntboundryCentralValAdj(j), 1:3000,'--g')
hold off hold off
x{j}= get(hgL{j}(2),'xdata') x{j}=get(hgL{j}(2),'xdata')
y{j}= get(hgL{j}(2),'ydata'); y{j}=get(hgL{j}(2),'ydata');
xb{j}=get(hgL{j}(1),'xdata') xb{j}=get(hgL{j}(1),'xdata')
yb{j}=get(hgL{j}(1),'ydata') yb{j}=get(hgL{j}(1),'ydata')
ybpostot{j}=sum(yb{j}(2,(xb{j}(1,:)>=0))) ybpostot{j}=sum(yb{j}(2,(xb{j}(1,:)>=0)))

20
workflow/apps/matlab/ezview/EZvInitLoad.m
View File

@@ -5,6 +5,7 @@ global Expbb
global userPars global userPars
global usrExpJobsDir global usrExpJobsDir
global zonePB global zonePB
global mpdmFile
% Initialize some variables from matlab % Initialize some variables from matlab
ezPath=which(mfilename); ezPath=which(mfilename);
@@ -22,7 +23,8 @@ end
% Set scansDir (project scans directory) intelligently % Set scansDir (project scans directory) intelligently
if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT')) if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
scansDir=getenv('PROJECT'); project=getenv('PROJECT');
fprintf('Using project path: %s from environment variable PROJECT\n', scansDir); fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
disp('This usually indicates that we are in standalone mode'); disp('This usually indicates that we are in standalone mode');
elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR')) elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
@@ -76,6 +78,19 @@ else
fprintf('Using EZview script directory: %s from hardcoded default\n', ezDir); fprintf('Using EZview script directory: %s from hardcoded default\n', ezDir);
end end
% Allow module to override hardcoded default EASY directory
if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
EASY_DIR=fullfile(getenv('EASY_DIR'));
if ~strcmp(easyDir, EASY_DIR) % sanity check
disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
easyDir=EASY_DIR;
end
fprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir);
else
fprintf('Using EASY script directory: %s from hardcoded default\n', easyDir);
end
userPars.BPdefault={'on','on','0.3','8','45','1000'}; userPars.BPdefault={'on','on','0.3','8','45','1000'};
userPars.boxplotFlg=1; userPars.boxplotFlg=1;
userPars.BPoutliers='On'; userPars.BPoutliers='On';
@@ -90,9 +105,6 @@ userPars.kfiltLim=str2double(userPars.BPdefault(6));
% Generate the Exp arrays % Generate the Exp arrays
numExps=3; numExps=3;
for i=1:numExps for i=1:numExps

7
workflow/apps/matlab/ezview/EZviewGui.m
View File

@@ -20,11 +20,6 @@ function varargout = EZviewGui(varargin)
% %
% See also: GUIDE, GUIDATA, GUIHANDLES % See also: GUIDE, GUIDATA, GUIHANDLES
gui_Singleton = 0; gui_Singleton = 0;
gui_State = struct( ... gui_State = struct( ...
'gui_Name', mfilename, ... 'gui_Name', mfilename, ...
@@ -66,7 +61,7 @@ function EZviewGui_OpeningFcn(hObject, eventdata, handles, varargin)
% so window can get raised using EZviewGui. % so window can get raised using EZviewGui.
if strcmp(get(hObject,'Visible'),'off') if strcmp(get(hObject,'Visible'),'off')
%plot(rand(5)); %plot(rand(5));
end end
% Special disabling of version for this later install of Matlab 2011a: % Special disabling of version for this later install of Matlab 2011a:

256
workflow/qhtcp-workflow
View File

@@ -586,32 +586,21 @@ easy() {
# TODO will need to play with the -sd startup option to see what works (well) # TODO will need to play with the -sd startup option to see what works (well)
# Skip this step altogether in auto mode since it requires graphical interaction # Skip this step altogether in auto mode since it requires graphical interaction
if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
export PROJECT_SCANS_DIR PROJECT_DATE EASY_DIR PROJECT_USER EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR MASTER_PLATE_FILE DRUG_MEDIA_FILE export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER PROJECT
echo "Hit enter to use the default EASY results directory $PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_($PROJECT_SUFFIX)" export EASY_DIR EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR
(( YES )) || read -r -p "Or enter a custom suffix: " suffix export MASTER_PLATE_FILE DRUG_MEDIA_FILE
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_${suffix:-$PROJECT_SUFFIX}"
while [[ -d $EASY_RESULTS_DIR ]]; do
count=1
if [[ $count -eq 1 ]] && ask "$EASY_RESULTS_DIR already exists, increment dir name (y) or overwrite (N)?"; then
EASY_SUFFIX="${suffix:-$PROJECT_SUFFIX}.$((count++))"
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
else
EASY_SUFFIX=${suffix:-$PROJECT_SUFFIX}
fi
done
EASY_SUFFIX=${EASY_SUFFIX:-$suffix:-$PROJECT_SUFFIX}
EASY_NAME="${PROJECT_PREFIX}_${EASY_SUFFIX}"
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_$EASY_NAME"
[[ -d $PROJECT_SCANS_DIR/MasterPlateFiles ]] || mkdir -p "$PROJECT_SCANS_DIR/MasterPlateFiles"
DRUG_MEDIA_FILE="$PROJECT_SCANS_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
MASTER_PLATE_FILE="$PROJECT_SCANS_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"
choose_easy_results_dir
DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
# Make EASY dirs # Make EASY dirs
debug "mkdir -p $EASY_RESULTS_DIR" debug "mkdir -p $EASY_RESULTS_DIR"
mkdir -p "$EASY_RESULTS_DIR" mkdir -p "$EASY_RESULTS_DIR"
dirs=('PrintResults' 'CFfigs' 'Fotos' 'Fotos/BkUp' 'matResults') dirs=('PrintResults' 'CFfigs' 'Fotos' 'Fotos/BkUp' 'matResults')
for d in "${dirs[@]}"; do for d in "${dirs[@]}"; do
debug "mkdir $EASY_RESULTS_DIR/$d"
mkdir "$EASY_RESULTS_DIR/$d" mkdir "$EASY_RESULTS_DIR/$d"
done done
@@ -619,13 +608,12 @@ easy() {
rsync -a "$EASY_DIR"/{figs,Ptmats} "$EASY_RESULTS_DIR" rsync -a "$EASY_DIR"/{figs,Ptmats} "$EASY_RESULTS_DIR"
# Launch matlab # Launch matlab
matlab -nosplash -r "run $script"
# matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script" # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
matlab -nosplash -r "run $script"
fi fi
# Use the function return code see if we succeeded # Use the function return code see if we succeeded
get_easy_results "$PROJECT_SCANS_DIR" || return 1 scan_easy_results "$PROJECT_SCANS_DIR" || (err "No EASY results found in $PROJECT_SCANS_DIR"; return 1)
} }
@@ -635,19 +623,17 @@ module ezview
ezview() { ezview() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER EZVIEW_DIR export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER EZVIEW_DIR
export EASY_RESULTS_DIR
EZVIEW_DIR="$APPS_DIR/matlab/ezview" EZVIEW_DIR="$APPS_DIR/matlab/ezview"
script="$EZVIEW_DIR/EZviewGui.m" script="$EZVIEW_DIR/EZviewGui.m"
# Try to load EASY output dir fromENV or easy module
# Then scan for EASY results
[[ -z $EASY_RESULTS_DIR ]] && choose_easy_results_dir
# Make EZview dirs # Make EZview dirs
debug "mkdir -p $EZVIEW_DIR"
matlab -nosplash -r "run $script" matlab -nosplash -r "run $script"
echo "$EZVIEW_DIR"
} }
@@ -714,12 +700,7 @@ module qhtcp
qhtcp() { qhtcp() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
OUT_DIR="/mnt/data/out/qhtcp"
STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
if [[ -d $QHTCP_PROJECT_DIR ]]; then if [[ -d $QHTCP_PROJECT_DIR ]]; then
echo "A project already exists at $QHTCP_PROJECT_DIR" echo "A project already exists at $QHTCP_PROJECT_DIR"
@@ -790,27 +771,8 @@ qhtcp() {
unset STUDY_DIR unset STUDY_DIR
# Replacing ExpFrontend.m # Replacing ExpFrontend.m
get_easy_results "$PROJECT_SCANS_DIR" || (err "No EASY results found in $PROJECT_SCANS_DIR"; return 1) choose_easy_results_dir
# Set the right results directory
# TODO eventually we could run this on multiple results dirs simultaneously with some refactoring
if ((YES)) || [[ ${#EASY_RESULTS_DIRS[@]} -eq 1 ]]; then
# In automatic mode just choose the first OUT DIR in the list
EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose the frist one
else
echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR"
echo "Here is a list: "
for (( i=0; i<${#EASY_RESULTS_DIRS[@]}; i++ )); do
printf "%d. %s\n" "$((i+1))" "${EASY_RESULTS_DIRS[i]}"
done
printf "%s\n" "${EASY_RESULTS_DIRS[@]}"
read -r -p "Enter the item number to select: " response
response=$(( response - 1 )) # bash arrays use zero indexing
EASY_RESULTS_DIR="${EASY_RESULTS_DIRS[$response]}"
fi
# TODO probably broken
EASY_RESULTS_FILES=("$EASY_RESULTS_DIR/"*"/PrintResults/!!"*)
# Create studies archive file if missing # Create studies archive file if missing
if ! [[ -d $STUDIES_ARCHIVE_FILE ]]; then if ! [[ -d $STUDIES_ARCHIVE_FILE ]]; then
header=(StudyDate tStudyName StudyPath ExpNum ExpDate ExpPath ResultFile) header=(StudyDate tStudyName StudyPath ExpNum ExpDate ExpPath ResultFile)
@@ -823,7 +785,7 @@ qhtcp() {
# Trying to match old ExpFrontend formatting # Trying to match old ExpFrontend formatting
printf "%s\t" \ printf "%s\t" \
"${DATE//_/}" "$PROJECT" "$QHTCP_PROJECT_DIR" "Exp$s" \ "${DATE//_/}" "$PROJECT" "$QHTCP_PROJECT_DIR" "Exp$s" \
"$PROJECT_DATE" "$PROJECT_SCANS_DIR" "$EASY_RESULT_DIR" "${f##*/}" \ "$PROJECT_DATE" "$PROJECT_SCANS_DIR" "$EASY_RESULTS_DIR" "${f##*/}" \
>> "$STUDIES_ARCHIVE_FILE" >> "$STUDIES_ARCHIVE_FILE"
done done
done done
@@ -1126,43 +1088,43 @@ r_gta_heatmaps() {
submodule mat_exp_frontend # submodule mat_exp_frontend
# @description Run the ExpFrontend.m program # # @description Run the ExpFrontend.m program
# This submodule: # # This submodule:
# * Pushes into the Study template directory (ExpTemplate) # # * Pushes into the Study template directory (ExpTemplate)
# * Prompts the user to run ExpFrontend.m # # * Prompts the user to run ExpFrontend.m
# * Pops out # # * Pops out
# NOTES: # # NOTES:
# * ExpFrontend.m should be or is being rewritten # # * ExpFrontend.m should be or is being rewritten
mat_exp_frontend() { # mat_exp_frontend() {
debug "Running: ${FUNCNAME[0]}" # debug "Running: ${FUNCNAME[0]}"
cat <<-EOF # cat <<-EOF
ExpFrontend.m was made for recording into a spreadsheet # ExpFrontend.m was made for recording into a spreadsheet
('StudiesDataArchive.txt') the date and files used (i.e., directory paths to the # ('StudiesDataArchive.txt') the date and files used (i.e., directory paths to the
!!Results files used as input for Z-interaction script) for each multi-experiment study. # !!Results files used as input for Z-interaction script) for each multi-experiment study.
Run the front end MATLAB programs in the correct order (e.g., run front end in "exp1" # Run the front end MATLAB programs in the correct order (e.g., run front end in "exp1"
folder to call the !!Results file for the experiment you named as exp1 in the StudyInfo.csv file) # folder to call the !!Results file for the experiment you named as exp1 in the StudyInfo.csv file)
The GTA and pairwise, TSHeatmaps, JoinInteractions and GTF Heatmap scripts use this table # The GTA and pairwise, TSHeatmaps, JoinInteractions and GTF Heatmap scripts use this table
to label results and heatmaps in a meaningful way for the user and others. # to label results and heatmaps in a meaningful way for the user and others.
The BackgroundSD and ZscoreJoinSD fields will be filled automatically according to user # The BackgroundSD and ZscoreJoinSD fields will be filled automatically according to user
specifications, at a later step in the QHTCP study process. # specifications, at a later step in the QHTCP study process.
COpen MATLAB and in the application navigate to each specific /Exp folder, # COpen MATLAB and in the application navigate to each specific /Exp folder,
call and execute ExpFrontend.m by clicking the play icon. # call and execute ExpFrontend.m by clicking the play icon.
Use the "Open file" function from within Matlab. # Use the "Open file" function from within Matlab.
Do not double-click on the file from the directory. # Do not double-click on the file from the directory.
When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder. # When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder.
Repeat this for every Exp# folder depending on how many experiments are being performed. # Repeat this for every Exp# folder depending on how many experiments are being performed.
The Exp# folder must correspond to the StudyInfo.csv created above. # The Exp# folder must correspond to the StudyInfo.csv created above.
EOF # EOF
script="ExpFrontend.m" # script="ExpFrontend.m"
if ! ((YES)) && # if ! ((YES)) &&
ask "Start MATLAB to run $script? This requires a GUI."; then # ask "Start MATLAB to run $script? This requires a GUI."; then
matlab -nosplash -r "$script" # matlab -nosplash -r "$script"
fi # fi
} # }
submodule r_interactions submodule r_interactions
@@ -1417,37 +1379,76 @@ get_studies() {
} }
submodule get_easy_results # lol submodule choose_easy_results_dir #
# @description Gets info about EASY output in the project's scans directory # @description Chooses an EASY scans directory if the information is undefined
# TODO: Standardize EASY output, it's hard to understand # TODO: Standardize EASY output, it's hard to understand
# @exitcode 0 if at least one results directory exists # TODO eventually we could run this on multiple results dirs simultaneously with some refactoring
# @exitcode 1 if no results directories exist # @exitcode 0 if successfully choose an EASY results dir
# @set EASY_RESULTS_DIRS array Globbed results files from PROJECT_SCANS_DIR/ # @set EASY_RESULTS_DIR string The working EASY output directory
# @set EASY_RESULTS_FILES array Globbed results files from PROJECT_SCANS_DIR/ choose_easy_results_dir() {
# @arg $1 string Project scans
get_easy_results() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
# Glob EASY output dirs declare -g EASY_RESULTS_DIR EASY_OUT_DIR
shopt -s nullglob
EASY_RESULTS_DIRS=( "$1"/Results*/ ) # TODO this is probably broken
[[ ${#EASY_RESULTS_DIRS} -ge 1 ]] || (echo "Missing EASY output"; return 1)
shopt -u nullglob
# This section is mostly to provide some example globbing EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy/"
declare -a EASY_RESULTS_ARRAY=()
for EASY_RESULTS_DIR in "${EASY_RESULTS_DIRS[@]}"; do # Don't override env
[[ -d $EASY_RESULTS_DIR ]] && echo "Found EASY Results directory: $EASY_RESULTS_DIR" if [[ -n $EASY_RESULTS_DIR && ! -d $EASY_RESULTS_DIR ]]; then
EASY_PRINT_RESULTS_DIR="$EASY_RESULTS_DIR/PrintResults" mkdir -p "$EASY_RESULTS_DIR"
[[ -d $EASY_PRINT_RESULTS_DIR ]] && echo "Found EASY PrintResults directory: $EASY_PRINT_RESULTS_DIR" return 0
EASY_PRINT_RESULTS_FILES=( fi
"$EASY_PRINT_RESULTS_DIR/!!"*
"$EASY_PRINT_RESULTS_DIR"/NoGrowth_*.txt local default_easy_results_dir="$EASY_OUT_DIR/$PROJECT"
"$EASY_PRINT_RESULTS_DIR"/GrowthOnly_*.txt
) if [[ -n $PROJECT ]]; then
EASY_RESULTS_ARRAY+=("$EASY_RESULTS_DIR" "$EASY_PRINT_RESULTS_DIR" "${EASY_PRINT_RESULTS_FILES[@]}") if [[ ! -d $default_easy_results_dir ]]; then
done EASY_RESULTS_DIR="$default_easy_results_dir"
[[ ${#EASY_RESULTS_DIRS[@]} -gt 0 ]] # TODO may need to change this to something more specific mkdir -p "$EASY_RESULTS_DIR"
return 0
fi
fi
# Always backup existing output
# This would happen if you ran the same experiment twice in one day, for instance
if [[ -d $default_easy_results_dir ]] ; then
backup_dir="$default_easy_results_dir"
while [[ -d $default_easy_results_dir ]]; do
count=1
backup_dir="$backup_dir.$((count++))"
done
echo "Backing up existing output from $default_easy_results_dir to $backup_dir"
debug "rsync -a $default_easy_results_dir $backup_dir"
rsync -a "$default_easy_results_dir" "$backup_dir" &&
EASY_RESULTS_DIR="$default_easy_results_dir"
fi
# echo "Hit enter to use the default EASY results directory: $default_easy_results_dir"
# if ! (( YES )); then
# read -r -p "Or enter a custom directory name, example: $PROJECT" dirname
# [[ -z $dirname ]] && EASY_RESULTS_DIR="$default_easy_results_dir" && return 0
# fi
# ((YES)) && return 0
# # Let's get a little fancy
# shopt -s nullglob
# declare -la easy_results_dirs=( "$easy_out_dir/"*/ )
# shopt -u nullglob
# # Sort the dirs
# mapfile -t easy_results_dirs < <(printf '%s\n' "${easy_results_dirs[@]}" | sort)
# last_index=$(( ${#easy_results_dirs} - 1 ))
# ((YES)) && EASY_RESULTS_DIR="${easy_results_dirs[$last_index]}" && return 0
# echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR"
# echo "Here is a list: "
# for i in "${!easy_results_dirs[@]}"; do
# printf "%d. %s\n" "$((i+1))" "${easy_results_dirs[i]}"
# done
# printf "%s\n" "${easy_results_dirs[@]}"
# last_index=$(( ${#easy_results_dirs} - 1 ))
# read -r -p "Enter the item number to select EASY results directory, default ($last_index): " response
# [[ -z $response ]] && response=$last_index
# response=$(( response - 1 )) # bash arrays use zero indexing
# EASY_RESULTS_DIR="${easy_results_dirs[$response]}"
# EASY_RESULTS_FILES=("$EASY_RESULTS_DIR/"*"/PrintResults/!!"*)
# [[ ${#easy_results_dirs[@]} -gt 0 ]]
} }
@@ -1482,13 +1483,20 @@ main() {
SCRIPT_DIR=$(dirname "$SCRIPT") SCRIPT_DIR=$(dirname "$SCRIPT")
# Global directory variables # Global directory variables
local out_heirarchy=("$OUT_DIR" "$SCRIPT_DIR/out" "/mnt/data/out")
for d in "${out_heirarchy[@]}"; do
if [[ -d $d ]]; then
debug "Using output directory: $d"
OUT_DIR="$d"
fi
done
TEMPLATES_DIR="$SCRIPT_DIR/templates" TEMPLATES_DIR="$SCRIPT_DIR/templates"
APPS_DIR="$SCRIPT_DIR/apps" APPS_DIR="$SCRIPT_DIR/apps"
DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
SCANS_HEIRARCHY=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans") # scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
SCANS_HEIRARCHY=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans") # search for a scans dir in this order (and fall back to default) local scans_heirarchy=( "$SCANS_DIR" "./scans" "/mnt/data/scans" "./scans") # TODO change back for production, avoid actual scan dirs during testing
# Find a scans directory # Find a scans directory
[[ -z $SCANS_DIR ]] && for d in "${SCANS_HEIRARCHY[@]}"; do [[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
if [[ -d $d ]]; then if [[ -d $d ]]; then
SCANS_DIR="$d" SCANS_DIR="$d"
fi fi
@@ -1555,11 +1563,17 @@ main() {
done done
# Loop over projects # Loop over projects
for PROJECT in "${PROJECTS[@]}"; do for PROJECT in "${PROJECTS[@]}"; do
declare -g PROJECT
PROJECT_SCANS_DIR="$SCANS/$PROJECT" PROJECT_SCANS_DIR="$SCANS/$PROJECT"
PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723 PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
PROJECT_SUFFIX="${PROJECT#????????_*_}" PROJECT_SUFFIX="${PROJECT#????????_*_}"
PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}" PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
# Run selected modules # Run selected modules
for m in "${MODULES[@]}"; do for m in "${MODULES[@]}"; do
ask "Run $m?" && "$m" ask "Run $m?" && "$m"