PCAPlot.m

function [COEFF,SCORE,latent] = PCAPlot(Matrix,Head,GeneName,d,N,dim)
%The input matrix is a gene X sample matrix
%             Sample1 Sample2 Sample3
%      gene1
%      gene2
%      gene3
%PCAPlot is a function to calculate PCs and plot out an image and .avi video
%The Matrix is to be transposed if you do Sample PCA for a gene table
%filtering and log transformation may have to be performed before using this function
%array d is required for specifying colors
%array Head is needed for labeling Sample Names
%This function depends on other functions in the same folder
%function [COEFF,SCORE,Latent] = PCAPlot(Matrix,Head,GeneName,d,N,dim)
%This function depends on discretize.m which only works on Matlab R2016b or later
%please run figure; first
if nargin < 6
    dim = 20;
end
if nargin < 5
    N=100
end
if nargin < 4
    error('Not enough input arguments.')
end

[COEFF,SCORE,latent] = pca(Matrix');
colormap(jet)
scatter3(SCORE(:,1),SCORE(:,2),SCORE(:,3),50,d,'filled');
ylabel(strcat('PC2(',strcat(num2str(round(latent(2)/sum(latent)*100)),'%'),')'))
zlabel(strcat('PC3(',strcat(num2str(round(latent(3)/sum(latent)*100)),'%'),')'))
xlabel(strcat('PC1(',strcat(num2str(round(latent(1)/sum(latent)*100)),'%'),')'))
text(SCORE(:,1)+0.5,SCORE(:,2)+0.5,SCORE(:,3)+0.5,Head);
%OptionZ.FrameRate=60;OptionZ.Duration=11;OptionZ.Periodic=true;
%CaptureFigVid([-20,10;-110,10;-190,80;-290,10;-380,10],'testvid.avi',OptionZ)
Index=COEFF; %This is just for getting the same dimentionality
[m n]=size(Matrix);
DIM=min(dim,n-1);
HeatMap(COEFF(:,1:DIM),'Displayrange',2.5,'Standardize',2,'colormap',colormap(jet))
figure
for i=1:min(DIM,30)                           
    subplot(5,6,i)
    scatter(SCORE(:,i),d,10,'.')
    title(strcat('PC',num2str(i)))
end
for i=1:DIM
    [test,Index(:,i)]=sort(COEFF(:,i));
    SaveCell([GeneName(Index(test<0,i)) Mat2StrArray(test(test<0))],strcat(num2str(i),'_neg.txt'));
    SaveCell(flipud([GeneName(Index(test>0,i)) Mat2StrArray(test(test>0))]),strcat(num2str(i),'_pos.txt'));
end

PlotSet=reshape(Index([1:N end:-1:end-N+1],1:3),6*N,1);
[Y1,E1]=discretize(COEFF(:,1),127);
[Y2,E2]=discretize(COEFF(:,2),127);
[Y3,E3]=discretize(COEFF(:,3),127);
JET=colormap(jet);
ColorCode=JET(max(ceil(abs([Y1 Y2 Y3]-64)+1)')',:);

figure;
scatter3(COEFF(:,1),COEFF(:,2),COEFF(:,3),20,ColorCode,'filled')
ylabel(strcat('PC2(',strcat(num2str(round(latent(2)/sum(latent)*100)),'%'),')'))
zlabel(strcat('PC3(',strcat(num2str(round(latent(3)/sum(latent)*100)),'%'),')'))
xlabel(strcat('PC1(',strcat(num2str(round(latent(1)/sum(latent)*100)),'%'),')'))
text(COEFF(PlotSet,1),COEFF(PlotSet,2),COEFF(PlotSet,3),GeneName(PlotSet))
pcascore=HeatMap(transpose(SCORE(:,DIM:-1:1)),'Standardize',2,'DisplayRange',2.5,'Symmetric','true','Colormap',colormap(jet),'RowLabels',[DIM:-1:1],'ColumnLabels',Head)
addTitle(pcascore,'PC scores')
figure;
donut([latent(1:DIM)' sum(latent(DIM+1:end)')],[strread(num2str([1:DIM]),'%s');{'Rest'}]',[],'pie')              
              
end