%load C:\Users\dan\Work\Datasets\Oncogenes\sigsummary.mat
%load ~/Work/Projects/FactorAnalysis/Data/Oncogenes/sigsummary.mat;
%load ~/Work/Projects/FactorAnalysis/Data/Oncogenes/all/sigsummaryall.mat;

[sortsigpids,sorti] = sort(sigpids);
sortsigs = sigmA(sorti,:).*sigmPostPib(sorti,:);%.*(sigmPostPib(sorti,:)>.95);
signzs = sigmPostPib(sorti,:)>.99;%(sortsigs~=0); % contains 1s for probes with nonzero signature loadings

%siglengths = sqrt(sum(sortsigs.*sortsigs));
%unitsortsigs = sortsigs./repmat(siglengths,8509,1);

[sortfacpids,sorti] = sort(pids(mVariablesIn));
facsig = mA(:,6:12).*mPostPib(:,6:12);
sortfacsig = facsig(sorti,:);
facnzs = mPostPib(sorti,6:12)>.99;%(sortfacsig~=0); %contains 1s for probes with nonzero factor loadings

% want to compare the F(:,n) to each of the 7 acidosis signatures for the
% set of overlapping genes
sigpidsindex = find(ismember(sortsigpids,sortfacpids)); %signature probe is in the factor probeset
signzs = signzs(sigpidsindex,:);

facpidsindex = find(ismember(sortfacpids,sortsigpids)); %factor probe is in the signature probeset
facnzs = facnzs(facpidsindex,:);

% compare signature factors with signatures
% first number is order in the signatures, second number is order in the
% factors
figure;
subplot(3,3,1);
% n-1hr is sig 1 and factor 2
scatter(sortsigs(sigpidsindex(~signzs(:,1) | ~facnzs(:,2)),1),sortfacsig(facpidsindex(~signzs(:,1) | ~facnzs(:,2)),2),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,1) & facnzs(:,2)),1),sortfacsig(facpidsindex(signzs(:,1) & facnzs(:,2)),2),30,[0,0,0],'+');hold off;
xlabel('n-1hr','FontSize',14);ylabel('f2','FontSize',14);
set(gca,'FontSize',14);
box off;

subplot(3,3,2);
% n-4hr is sig 2 and factor 1
scatter(sortsigs(sigpidsindex(~signzs(:,2) | ~facnzs(:,1)),2),sortfacsig(facpidsindex(~signzs(:,2) | ~facnzs(:,1)),1),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,2) & facnzs(:,1)),2),sortfacsig(facpidsindex(signzs(:,2) & facnzs(:,1)),1),30,[0,0,0],'+');hold off;
xlabel('n-4hr','FontSize',14);ylabel('f1','FontSize',14);
set(gca,'FontSize',14);
box off;

subplot(3,3,3);
%-n1hr is sig 3 and factor 3
scatter(sortsigs(sigpidsindex(~signzs(:,3) | ~facnzs(:,3)),3),sortfacsig(facpidsindex(~signzs(:,3) | ~facnzs(:,3)),3),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,3) & facnzs(:,3)),3),sortfacsig(facpidsindex(signzs(:,3) & facnzs(:,3)),3),30,[0,0,0],'+');hold off;
xlabel('-n1hr','FontSize',14);ylabel('f3','FontSize',14);
set(gca,'FontSize',14);
box off;

subplot(3,3,4);
%-n4hr is sig 4 and factor 7
scatter(sortsigs(sigpidsindex(~signzs(:,4) | ~facnzs(:,7)),4),sortfacsig(facpidsindex(~signzs(:,4) | ~facnzs(:,7)),7),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,4) & facnzs(:,7)),4),sortfacsig(facpidsindex(signzs(:,4) & facnzs(:,7)),7),30,[0,0,0],'+');hold off;
xlabel('-n4hr','FontSize',14);ylabel('f7','FontSize',14);
set(gca,'FontSize',14);
box off;

%--1hr is sig 5 and factor 6
subplot(3,3,5);
scatter(sortsigs(sigpidsindex(~signzs(:,5) | ~facnzs(:,6)),5),sortfacsig(facpidsindex(~signzs(:,5) | ~facnzs(:,6)),6),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,5) & facnzs(:,6)),5),sortfacsig(facpidsindex(signzs(:,5) & facnzs(:,6)),6),30,[0,0,0],'+');hold off;
xlabel('--1hr','FontSize',14);ylabel('f6','FontSize',14);
set(gca,'FontSize',14);
box off;

%--4hr is sig 6 and factor 5
subplot(3,3,6);
scatter(sortsigs(sigpidsindex(~signzs(:,6) | ~facnzs(:,5)),6),sortfacsig(facpidsindex(~signzs(:,6) | ~facnzs(:,5)),5),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,6) & facnzs(:,5)),6),sortfacsig(facpidsindex(signzs(:,6) & facnzs(:,5)),5),30,[0,0,0],'+');hold off;
xlabel('--4hr','FontSize',14);ylabel('f5','FontSize',14);
set(gca,'FontSize',14);
box off;

%n--4hr is sig 7 and factor 4
subplot(3,3,8);
scatter(sortsigs(sigpidsindex(~signzs(:,7) | ~facnzs(:,4)),7),sortfacsig(facpidsindex(~signzs(:,7) | ~facnzs(:,4)),4),30,[.5,.5,.5]);hold on;
scatter(sortsigs(sigpidsindex(signzs(:,7) & facnzs(:,4)),7),sortfacsig(facpidsindex(signzs(:,7) & facnzs(:,4)),4),30,[0,0,0],'+');hold off;
xlabel('n--4hr','FontSize',14);ylabel('f4','FontSize',14);
set(gca,'FontSize',14);
box off;

set(gcf,'Units','inches','Position',[2,2,8,8]); % one way to set the dimensions of the figure




%end;