Question

I have 3 groups of data that had PCA performed on them as one group. I want to highlight each variable group with a different color. Prior to this I overlaid 3 biplots. This gives different colors but creates a distortion in the data as each biplot function skews the data. This caused the groups to all be skewed by different amounts, making the plot not a correct representation.

How do I take a PCA scores matrix (30×3) and split it so the first 10×3 is one color, the next 10×3 is another and the third 10×3 is another, without the data being skewed?

Answer 1

This is the method I used to plot biplot data with different colors. The lines of code prior to plot are taken from the biplot.m file. The way biplot manipulates data is kept intact and stops skewing of data when using overlaid biplots.

This coding is not the most efficient, one can see parts that can be cut. I wanted to keep the code intact so one can see how biplot works in it’s entirety.

%%%%%%%%%%%%%%%%%%%%%

xxx = coeff(:,1:3); 
yyy= score(:,1:3);

**%Taken from biplot.m; This is alter the data the same way biplot alters data - having the %data fit on grid axes no larger than 1.**

[n,d2] = size(yyy);  
[p,d] = size(xxx); %7 by 3  
[dum,maxind] = max(abs(xxx),[],1);  
colsign = sign(xxx(maxind + (0:p:(d-1)*p)));  
xxx = xxx .* repmat(colsign, p, 1);  
yyy= (yyy ./ max(abs(yyy(:)))) .* repmat(colsign, 42, 1);  
nans = NaN(n,1);  

ptx = [yyy(:,1) nans]';  
pty = [yyy(:,2) nans]';  
ptz = [yyy(:,3) nans]';  

**%I grouped the pt matrices for my benefit** 

plotdataholder(:,1) = ptx(1,:);  
plotdataholder(:,2) = pty(1,:);  
plotdataholder(:,3) = ptz(1,:);  

**%my original score matrix is 42x3 - wanted each 14x3 to be a different color**

scatter3(plotdataholder(1:14,1),plotdataholder(1:14,2),plotdataholder(1:14,3),35,[1 0 0],'marker', '.');   
hold on;  
scatter3(plotdataholder(15:28,1),plotdataholder(15:28,2),plotdataholder(15:28,3),35,[0 0 1],'marker', '.') ;  
scatter3(plotdataholder(29:42,1),plotdataholder(29:42,2),plotdataholder(29:42,3),35,[0 1 0],'marker', '.');   
xlabel('Principal Component 1');  
ylabel('Principal Component 2');  
zlabel('Principal Component 3');