Indexing scores to plot pca results in biplot

I am trying to visualize the results of a principal component analysis using biplot. I want to color the data by site (or time intervals, etc). Let's take coloring the results by site as an example: In this case the first half of the data (first 4629 rows in the scores output from the pca function) is for site 1 and the second half for site 2 (rows 4630 to the end in the scores output).

When I plot all of the data in gray (circles) and the sites in colors (points), the first site (blue) doesn't line up with the gray points and I can't figure out why.

Am I indexing the score values correctly if score is a 9258x8 double and I want to plot the first 4629 rows (site 1) in blue then the second 4629 rows (site 2) in red?

X = horzcat(DO_s,O2sat_s,PH_s,Temp_s,Sal_s,Depth_s,PAR_s,absVel_s);

[coeff,score,latent,tsquared] = pca(X);

f4=figure(4)

hold on; box on;

biplot(coeff(:,1:2),'scores',score(:,1:2),'color','k','Marker','o','markeredgecolor',[.9 .9 .9])

biplot(coeff(:,1:2),'scores',score(1:4629,1:2),'color','k','Marker','.','markeredgecolor','b','varlabels',...

{'DO','O2sat','pH','Temp','Sal','Depth','PAR','|Velocity|'}); %Site 1 (1:4629)

biplot(coeff(:,1:2),'scores',score(4630:end,1:2),'color','k','Marker','.','markeredgecolor','r') %Site 2 (4630:end)

yline(0,'--')

xline(0,'--')

title('Full Deployment');

set(gca,'fontsize',18)

[Heidi Hirsh]

I've done a lot of experimenting with indexing and it looks like the indexed subset of data is always rescaled (doesn't plot to the same positions as the original (gray) data UNLESS I index some value to the end. For instance score(4630:end,1:2) works but score(4630:9257,1:2) moves the points. if I look at the paired numbers in each they are the same (one more for the former) so I think it must be a plotting error. Has anyone successfully indexed score data?

[Heidi Hirsh]

I think I did it!

I used this post: https://www.mathworks.com/matlabcentral/answers/458470-coloring-the-dots-in-biplot-chart

My code now reads:

X = horzcat(DO_s,O2sat_s,PH_s,Temp_s,Sal_s,Depth_s,PAR_s,absVel_s);

[coeff,score,latent,tsquared,explained] = pca(X);

subgroup1 = repmat(1,length(time),1); %first 4629 (1:4629) points are MSP1

subgroup2 = repmat(2,length(time),1); %second 4629 (4630:end) are MSP2

site = vertcat(subgroup1,subgroup2);

close all

% %figure out how to color MSP1 versus MSP2

% color2 = [1 .6 .6]

% color1 = [.4 .6 1]

f4=figure(4) %scaled data

hold on; box on;

% biplot(coeff(:,1:2),'scores',score(:,1:2),'color','Marker','o','markeredgecolor',[.7 .7 .7]);

h= biplot(coeff(:,1:2),'scores',score(:,1:2),'color','k','varlabels',...

{'DO','O2sat','pH','Temp','Sal','Depth','PAR','|Velocity|'});

%color by site

hID = get(h,'tag'); %identify handle

hPt = h(strcmp(hID,'obsmarker')); %isolate handles to scatter points

grp = findgroups(site);

grpID = 1:max(grp);

clrMap = winter(length(unique(grp)));

for i = 1:max(grp)

set(hPt(grp==i), 'Color', clrMap(i,:), 'DisplayName', sprintf('MSP%d', grpID(i)))

end

yline(0,'--')

xline(0,'--')

title('Full Deployment');

set(gca,'fontsize',18)

%legend for color

[~, unqIdx] = unique(grp);

legend(hPt(unqIdx))