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ImageStream_Heatmaps_V4_20200115.m
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ImageStream_Heatmaps_V4_20200115.m
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%Name: ImageStream_Heatmaps_V4
%Date last modified: 2020/01/15
%Authors: Gautam Dey, Scott Curran
%Goal: Generate heatmaps from ImageStream data
%%%%%%%
%initialise
clear; %close all
%load parameters
indir='/Users/gautam/Dropbox/Collaborations/Pombe Segmentation files/Heatmaps/Jan 2020/';
namefrag='S';
loadfulldata=0;
binfulldata=0;
sortdata=1;
numstrains=49;
numcutoff=500;
load ([indir 'StrainGroups.mat']);
%% concatenate
if loadfulldata==0
load([indir 'ImageStream-RawData-20200115.mat']);
%find extents
FullStrainData=struct;
for nStrain=1:numstrains
StrainName=['= ' namefrag num2str(nStrain) ';'];
TempVar=genvarname('TempVar');
eval([TempVar StrainName]);
FullStrainData(nStrain).data=TempVar;
disp(nStrain)
end
save([indir 'FullStrainData.mat'],'FullStrainData');
end
%% Various binning
if binfulldata==0
load([indir 'FullStrainData.mat']);
StrainNameVec={}; LengthBinTot=[]; SeptVec=[];
for nStrain=1:numel(FullStrainData)
D=FullStrainData(nStrain).data;
Dmat=D{:,1:4};
SeptVec=[SeptVec; D{3,7}];
SN=D.Properties.VariableNames;
StrainNameVec{nStrain}=SN{7}; %#ok<*SAGROW>
%keyboard
LengthBinTot=[LengthBinTot; Dmat(:,1)]; %#ok<*AGROW>
end
LengthBinTot=unique(LengthBinTot);
LengthBinTot=LengthBinTot(~isnan(LengthBinTot));
%correction
StrainNameVec{22}='SC265';
%Concatenate all strains
IntMat=[]; IntMatRaw=[]; SDMat=IntMat; CountMat=IntMat; StrCntr=0;
for nStrain=1:numel(FullStrainData)
%strain matching
StrMatch=strcmp(Strain,StrainNameVec{nStrain});
%keyboard
if sum(StrMatch)==1
StrMatch=find(StrMatch==1);
StrCntr=StrCntr+1;
D=FullStrainData(nStrain).data; Dmat=D{:,1:4};
IntMatRaw(nStrain)=sum(Dmat(:,2));
%keyboard
for nBin=1:numel(LengthBinTot)
binidx=find(Dmat(:,1)==LengthBinTot(nBin));
%get minimum value for normalization
minidx=find(Dmat(:,4)>500);
minval=min(Dmat(minidx,2));
if ~isempty(binidx) && Dmat(binidx,4)>500 %remove bins <500
IntMat(StrMatch,nBin)=Dmat(binidx,2)./minval;
SDMat(StrMatch,nBin)=Dmat(binidx,3)./minval;
CountMat(StrMatch,nBin)=Dmat(binidx,4)./sum(Dmat(:,4));
else
IntMat(StrMatch,nBin)=NaN;
SDMat(StrMatch,nBin)=NaN;
CountMat(StrMatch,nBin)=NaN;
end
end
end
end
save([indir 'RawHeatMap.mat'],'IntMat','SDMat','CountMat','LengthBinTot','StrainNameVec','SeptVec','IntMatRaw');
end
% subplot(1,2,1)
% imagesc(IntMat); colormap gray
% subplot(1,2,2)
% imagesc(CountMat); colormap gray
%%
if sortdata==0
load([indir 'RawHeatMap.mat']);
%sort by count
%IntCountMat=zeros(numstrains,60);
IntSeptMat=zeros(numstrains,60);
for nStrain=1:numstrains
[mval,countidx]=max(CountMat(nStrain,:));
septidx=find(LengthBinTot>SeptVec(nStrain),1);
% Stval1=30-countidx; Enval1=(Stval1+numel(LengthBinTot))-1;
% IntCountMat(nStrain,Stval1:Enval1)=IntMat(nStrain,:);
%
Stval2=50-septidx; Enval2=(Stval2+numel(LengthBinTot))-1;
IntSeptMat(nStrain,Stval2:Enval2)=IntMat(nStrain,:);
%sortvec=1:size(CountMat,2); sortvec=sortvec-countidx;
%plot(sortvec,CountMat(nStrain,:),'-'); hold on
%plot(sortvec,IntMat(nStrain,:),'-'); hold on
end
end
%% plotting routines
%sets (see notes)
keepset1=find(Group==1);
keepset2=find(Group==2); keepset2=setdiff(keepset2,[34 38]);
keepset3=find(Group==3);
%keepset1=setdiff(1:47,[34 38]);
figure;
imagesc(IntMat(keepset1,2:49)); colorbar; title ('Aligned by length'); caxis([0.8 2]); %caxis([0.8 2.5]);
yticks(1:length(keepset1));
yticklabels(Genotype(keepset1));
xticktotalvec=LengthBinTot(2:49); %xticktotalvec=xticktotalvec+1;
xticks([2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47]+1);
xticklabels(xticktotalvec(xticks));
%colormap(brewermap([],'*RdBu'))
colormap(brewermap([],'*Spectral'))
%colormap(brewermap([],'*PuBu'))
figure; subplot(2,1,1)
imagesc(IntMat(keepset2,2:49)); colorbar; title ('Aligned by length'); caxis([0.8 2]); %caxis([0.8 2.5]);
yticks(1:length(keepset2));
yticklabels(Genotype(keepset2));
xticktotalvec=LengthBinTot(2:49); %xticktotalvec=xticktotalvec+1;
xticks([2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47]+1);
xticklabels(xticktotalvec(xticks));
%colormap(brewermap([],'*RdBu'))
%colormap(brewermap([],'*PuBu'))
colormap(brewermap([],'*Spectral'))
subplot(2,1,2)
imagesc(IntMat(keepset3,2:49)); colorbar; title ('Aligned by length'); caxis([0.8 2.5]); %caxis([0.8 2.5]);
yticks(1:length(keepset3));
yticklabels(Genotype(keepset3));
xticktotalvec=LengthBinTot(2:49); %xticktotalvec=xticktotalvec+1;
xticks([2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47]+1);
xticklabels(xticktotalvec(xticks));
%colormap(brewermap([],'*RdBu'))
%colormap(brewermap([],'*PuBu'))
colormap(brewermap([],'*Spectral'))