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plotSignalCluster.m
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plotSignalCluster.m
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close all; clear all; clc;
alldata = [];
names = [];
groupColor = [];
groupNo = [];
cellFate = [];
field = 1;
outputsignalNo =1;
searchInd(1,:) = [1 1 1 1 1 1 1 3 3 3 3 ];
searchInd(2,:) = [3 4 5 6 7 8 9 3 4 5 6 ];
selectedparams = 17:29;
%searchInd(1,:) = [3 3 3 3 ];
%searchInd(2,:) = [3 4 5 6 ];
%searchInd(1,:) = [1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 5 6 7 8];
%searchInd(2,:) = [3 5 7 8 9 3 5 7 8 9 3 4 5 6 7 3 4 5 6 7 10 10 10 10];
mycolor = [hsv(5);hsv(5);hsv(5);hsv(5);hsv(5)];%size(searchInd,2));
mycolor2 = hsv(3);
ndpathname = 'c:\computation\02-03-2013';
%ndpathname = 'E:\data';
noCluster = 20;
%ndpathname = '/home/ss240/files/ImStor/sorger/data/NIC/Pat/02-03-2013/';
data_index = 1;
for i = 1:size(searchInd,2)
row = searchInd(1,i);
col = searchInd(2,i);
H5filename = ['H5OUT_r' num2str(row) '_c' num2str(col) '.h5'];
param_name = ['/field' num2str(field) '/clusterparams' num2str(outputsignalNo)];
signal_name = ['/field' num2str(field) '/outputsignal' num2str(outputsignalNo)];
timestamp_name = ['/field' num2str(field) '/timestamp' num2str(outputsignalNo)];
sisterList_name = ['/field' num2str(field) '/sisterList'];
fid = H5F.open(fullfile(ndpathname,H5filename),'H5F_ACC_RDWR','H5P_DEFAULT');
if H5L.exists(fid,param_name,'H5P_DEFAULT')
H5F.close(fid);
paraminfo = h5info(fullfile(ndpathname,H5filename), param_name);
startind = double([1 1]);
countind = [paraminfo.Dataspace.Size(1) paraminfo.Dataspace.Size(2)];
param_mat = double(h5read(fullfile(ndpathname,H5filename),param_name,startind, countind));
alldata = [alldata;param_mat];
groupNo = [groupNo;i*ones(size(param_mat,1),1)];
signalinfo = h5info(fullfile(ndpathname,H5filename), signal_name);
%sisterListinfo = h5info(fullfile(handles.SourceF,H5filename), sisterList_name);
%sisterList = h5read(fullfile(handles.SourceF,H5filename),sisterList_name,[1 1 1],...
% [sisterListinfo.Dataspace.Size(1) sisterListinfo.Dataspace.Size(2) sisterListinfo.Dataspace.Size(3)]);
startind = double([1 1 2]);
countind = [signalinfo.Dataspace.Size(1) signalinfo.Dataspace.Size(2) 1];
signal = permute(h5read(fullfile(ndpathname,H5filename),signal_name,startind, countind),[2 1 3]);
timestamp = h5read(fullfile(ndpathname,H5filename),timestamp_name);
for c_cell=1:size(param_mat,1)
PosTime = find(signal(:,param_mat(c_cell,1)));
tempData = zeros(1,length(timestamp));
originData(data_index,:) = signal(:,param_mat(c_cell,4))';
%figure(1), plot(timestamp(PosTime),originData(data_index,PosTime),'r-');drawnow;
data_index = data_index+1;
names{length(names)+1} = ['r' num2str(row) 'c' num2str(col) '_' num2str(param_mat(c_cell,1))];
groupColor = [groupColor;mycolor(i,:)];
cellFate = [cellFate;param_mat(c_cell,30)];
end
clear param_mat;
else
H5F.close(fid);
end
end
[R C] = find(originData==0);
for i=1:length(R)
originData(R(i),C(i)) = NaN;
end
w = 1./nanvar(alldata(:,selectedparams));
w(w==inf) = 1e-64;
[wcoeff,score,latent,tsquared,explained] = pca(alldata(:,selectedparams),'VariableWeights',w);
%c3 = wcoeff(:,1:3)
coefforth = diag(sqrt(w))*wcoeff;
cscores = zscore(alldata(:,selectedparams))*coefforth;
figure(1)
gscatter(score(:,1),score(:,2),cellFate,'bgrkm','ssxoo',3,'on','1st Principal Component','2nd Principal Component');
xlabel('1st Principal Component');
ylabel('2nd Principal Component');
figure(14)
interestedG = 6;
gscatter(score(groupNo==interestedG,1),score(groupNo==interestedG,2),cellFate(groupNo==interestedG),mycolor2,'x',3,'on','1st Principal Component','2nd Principal Component');
xlabel('1st Principal Component');
ylabel('2nd Principal Component');
plotG = 6;
figure(15);set(gcf,'Position',[500 500 400 400]);
myX = 1;
myY = 2;
gscatter(score(groupNo~=plotG,myX),score(groupNo~=plotG,myY),groupNo(groupNo~=plotG),[0.6 0.6 0.6],'o',2.5,'off');
hold on;
gscatter(score(groupNo==plotG-1,myX),score(groupNo==plotG-1,myY),groupNo(groupNo==plotG-1),[0 1 0],'o',2.5,'off');
gscatter(score(groupNo==plotG-2,myX),score(groupNo==plotG-2,myY),groupNo(groupNo==plotG-2),[0 0 0],'o',2.5,'off');
gscatter(score(groupNo==plotG+1,myX),score(groupNo==plotG+1,myY),groupNo(groupNo==plotG+1),[0 0 1],'o',2.5,'off');
gscatter(score(groupNo==plotG,myX),score(groupNo==plotG,myY),groupNo(groupNo==plotG),[1 0 0],'o',2.5,'off','1st Principal Component','2nd Principal Component');
axis equal;
figure(16);
plotG = 1:7;
mycolor3=jet(length(plotG));
for i=plotG
plot(nanmean(originData(groupNo==i,:),1),'color',mycolor3(i-plotG(1)+1,:)); hold on
mylegend{i-plotG(1)+1} = ['r' num2str(searchInd(1,i)) 'c' num2str(searchInd(2,i))];
end
hold off;
legend(mylegend);
%gname(names)
figure(2);
pareto(explained);
xlabel('Principal Component');
ylabel('Variance Explained (%)');
[st2,index] = sort(tsquared,'descend'); % sort in descending order
extreme = index(1:10);
figure(3);
biplot(coefforth(:,1:2),'scores',score(:,1:2),'varlabels',num2str((1:size(alldata(:,selectedparams),2))'));
figure(6);
for i=1:4%size(wcoeff,2)
subplot(2,2,i),bar(coefforth(:,i));
title(['Component' num2str(i)]);
end
figure(5);
biplot(coefforth(:,1:3),'scores',score(:,1:3),'varlabels',num2str((1:size(alldata(:,selectedparams),2))'),'Marker','x');
hold off;
%axis([-.26 0.8 -.51 .51 -.61 .81]);
%view([30 40]);
figure(4),
scatter3(score(:,1),score(:,2),score(:,3),22,groupColor);
xlabel('1st Principal Component');
ylabel('2nd Principal Component');
zlabel('3rd Principal Component');
Z = linkage(score(:,1:8),'ward','euclidean');
T = cluster(Z,'maxclust',noCluster);
%T = kmeans(score(:,1:2),noCluster,'replicates',4);
%
%
mycolor = hsv(noCluster);
figure(7)
scatter3(score(:,1),score(:,2),score(:,3),22,mycolor(T,:),'x');
xlabel('1st Principal Component');
ylabel('2nd Principal Component');
zlabel('3rd Principal Component');
figure(10)
gscatter(score(:,1),score(:,2),T,mycolor,'osv',3,'on','1st Principal Component','2nd Principal Component');
%figure(8);
%D = pdist(score(:,1:3),'euclidean');
%leafOrder = optimalleaforder(Z,D);
%[H,T2,outperm] = dendrogram(Z,0,'Labels',num2str(T),'Orientation','left','ColorThreshold',60); % ,'Reorder',leafOrder
%figure(9);
%load MyColormaps
%heatmap(mat2gray(originData(outperm,:),[0.9 1.5]),[],T,[],...
% 'ColorLevels',128,'Colormap',mycmap1,'FontSize',1);
binning = [];
for i=1:size(searchInd,2)
binSize=[];
for j=1:noCluster
binning{i,j} = find(groupNo==i & T==j);
binSize(j) = numel(binning{i,j});
end
figure(20); subplot(3,7,i);
bar(1:noCluster,binSize);
title(['Row:' num2str(searchInd(1,i)) ', Col:' num2str(searchInd(2,i))]);
xlim([0 noCluster+1]);%ylim([0 0.8]);
end
clear refGroupList myList1 taken_myList1 n x temp sizeTaken newList
refGroup = 1;
refGroupList = T(groupNo==refGroup);
uniqueCluster = unique(refGroupList);
temp = zeros(length(uniqueCluster),2);
for i=1:length(uniqueCluster)
temp(i,1) = uniqueCluster(i);
temp(i,2) = length(find(refGroupList==uniqueCluster(i)));
end
sizeTaken =length(uniqueCluster);
myList1 = flipud(sortrows(temp,2));
if size(myList1,1)<sizeTaken
taken_myList1 = myList1(1:size(myList1,1),1)';
else
taken_myList1 = myList1(1:sizeTaken,1)';
end
clear refGroupList taken_myList2 temp sizeTaken2
refGroup = 7;
refGroupList = T(groupNo==refGroup);
uniqueCluster = unique(refGroupList);
temp2 = zeros(length(uniqueCluster),2);
for i=1:length(uniqueCluster)
temp2(i,1) = uniqueCluster(i);
temp2(i,2) = length(find(refGroupList==uniqueCluster(i)));
end
sizeTaken2 =length(uniqueCluster);
myList2 = flipud(sortrows(temp2,2));
if size(myList1,1)<sizeTaken2
taken_myList2 = myList2(1:size(myList2,1),1)';
else
taken_myList2 = myList2(1:sizeTaken2,1)';
end
clear newList;
newList = zeros(1,noCluster);
FrontI = 1;
BackI = noCluster;
for i=1:max([length(taken_myList1) length(taken_myList2)])
if i<=length(taken_myList1) && isempty(find(newList==taken_myList1(i),1))
newList(FrontI) = taken_myList1(i);
taken_myList2 = taken_myList2(taken_myList2~=taken_myList1(i));
FrontI=FrontI+1;
end
if i<=length(taken_myList2) && isempty(find(newList==taken_myList2(i),1))
newList(BackI) = taken_myList2(i);
taken_myList1 = taken_myList1(taken_myList1~=taken_myList2(i));
BackI=BackI-1;
end
end
emptyInd = find(newList==0);
emptyValue = setdiff(1:noCluster,newList);
for i=1:length(emptyInd)
newList(emptyInd(i)) = emptyValue(i);
end
k = 1;
for i=1:size(searchInd,2)
countInd=1;
binSize=[];
for j=newList
binSize(countInd) = numel(binning{i,j});
countInd=countInd+1;
end
figure(20); subplot(3,7,k);
k = k+1;
h=bar(1:noCluster,binSize/sum(binSize));
set(gca,'XTickLabel',[]);
%text(1:noCluster,0.2*ones(1,noCluster),str2num(newList'));
xlim([0 noCluster+1]); ylim([0 0.7]);
title(['Row:' num2str(searchInd(1,i)) ', Col:' num2str(searchInd(2,i))]);
end
% [clusterInfo, pointToClusterMap] = MeanShiftClustering(score(:,1:2),0.1);
% plotMeanShiftResult(score(:,1:2),clusterInfo,pointToClusterMap);
% binning = [];
%
% noC = size(clusterInfo,2)
% for i=1:size(searchInd,2)
% binSize=[];
% for j=1:noC
% binning{i,j} = find(groupNo==i & pointToClusterMap==j);
% binSize(j) = numel(binning{i,j});
% end
% figure(11); subplot(4,5,i);
% bar(1:noC,binSize);
% title(['Row:' num2str(searchInd(1,i)) ', Col:' num2str(searchInd(2,i))]);
% %xlim([0 noC+1]);%ylim([0 0.8]);
% end
% clear myList1 taken_myList1 n x temp sizeTaken newList1 newList2
%
% refGroup = 1;
%
% [n x] = hist(pointToClusterMap(groupNo==refGroup),unique(pointToClusterMap(groupNo==refGroup))');
% temp(:,1) = x';
% temp(:,2) = n';
%
% sizeTaken =round(length(unique(pointToClusterMap(groupNo==refGroup))));
% myList1 = flipud(sortrows(temp,2));
% if size(myList1,1)<sizeTaken
% taken_myList1 = myList1(1:size(myList1,1),1)';
% else
% taken_myList1 = myList1(1:sizeTaken,1)';
% end
%
% clear myList2 taken_myList2 n2 x2 temp2 sizeTaken2
%
% refGroup = 5;
%
% [n2 x2] = hist(pointToClusterMap(groupNo==refGroup),unique(pointToClusterMap(groupNo==refGroup))');
% temp2(:,1) = x2';
% temp2(:,2) = n2';
%
% sizeTaken2 =round(length(unique(pointToClusterMap(groupNo==refGroup))));
% myList2 = flipud(sortrows(temp2,2));
% if size(myList1,1)<sizeTaken2
% taken_myList2 = myList2(1:size(myList2,1),1)';
% else
% taken_myList2 = myList2(1:sizeTaken2,1)';
% end
% newList1 = zeros(1,noC);
% newList2 = zeros(1,noC);
% FrontI = 1;
% BackI = 1;
% for i=1:max([length(taken_myList1) length(taken_myList2)])
%
% if i<=length(taken_myList1)
%
% if isempty(find(newList2==taken_myList1(i),1))
% newList1(FrontI) = taken_myList1(i);
% FrontI=FrontI+1;
% % elseif (find(newList1==taken_myList1(i)) <= find(newList2==taken_myList1(i),1)) && temp(taken_myList1(i)==temp(:,1),2)/sum(n1) > temp2(taken_myList1(i)==temp2(:,1),2)/sum(n2)
% %
% % newList2(newList2==taken_myList1(i),1)=0;
% % newList2 = newList2(newList2~=0);
% % newList1(FrontI) = taken_myList1(i);
% % FrontI=FrontI+1;
% % BackI=BackI-1;
% end
%
% end
%
% if i<=length(taken_myList2)
% if isempty(find(newList1==taken_myList2(i),1))
% newList2(BackI) = taken_myList2(i);
% BackI=BackI+1;
% % elseif (find(newList2==taken_myList2(i)) <= find(newList1==taken_myList2(i),1)) && temp2(taken_myList2(i)==temp2(:,1),2)/sum(n2) > temp(taken_myList2(i)==temp(:,1),2)/sum(n1)
% %
% % newList1(newList1==taken_myList2(i),1)=0;
% % newList1 = newList1(newList1~=0);
% %
% % newList2(BackI) = taken_myList2(i);
% % BackI=BackI+1;
% % FrontI=FrontI-1;
% end
%
% end
%
% end
% newList2 = fliplr(newList2);
% newList = zeros(1,noC);
% newList(newList1~=0) = newList1(newList1~=0);
% newList(newList2~=0) = newList2(newList2~=0);
%
% %emptyInd = sort(find(newList==0));
% %
% % refGroup = 14;
% % clear taken_myList3 n3 x3 temp3
% % [n3 x3] = hist(pointToClusterMap(groupNo==refGroup),unique(pointToClusterMap(groupNo==refGroup))');
% % collectL = [];
% % for i=1:length(x3)
% % if ~isempty(find(x3(i) == intersect(x3,emptyInd),1))
% % collectL = [collectL i];
% % end
% % end
% %
% % temp3(:,1) = x3(collectL)';
% % temp3(:,2) = n3(collectL)';
% % taken_myList3 = flipud(sortrows(temp3,2))';
% %
% % newList(emptyInd(1):(emptyInd(1)+length(taken_myList3)-1)) = taken_myList3(1,:)
%
% newList(newList==0) = setdiff(1:noC,find(newList~=0));
%
% k = 1;
% for i=1:size(searchInd,2)
%
% countInd=1;
% binSize=[];
% for j=newList
% binSize(countInd) = numel(binning{i,j});
% countInd=countInd+1;
% end
%
% figure(11); subplot(4,5,k);
% k = k+1;
% h=bar(1:noC,binSize/sum(binSize));
% set(gca,'XTickLabel',[]);
% %text(1:noCluster,0.2*ones(1,noCluster),str2num(newList'));
%
% xlim([0 noC+1]); ylim([0 0.2]);
% title(['Row:' num2str(searchInd(1,i)) ', Col:' num2str(searchInd(2,i))]);
% end