MATLAB: Coloring The Dots in biPlot Chart

biplot

I have created biplot as below and I'm looking for a way to distinguish the dots by different colors according to their group name. There are 12 groups and here are mydata and codes.

categories = ['F1';'F2';'F3';'F4';'F5';'F6';'F7';'F8'];
load('MAT_ALL.mat')
figure(1)
[coefforth,score,~,~,explainedVar] = pca(MaT_All(:,9:16));
load('DataGroup.mat')
clusters = DataGroup(:,20);
[coefforth,score,~,~,explainedVar] = pca(MaT_All(:,9:16));
figure(3)
biplot([coefforth(:,1) coefforth(:,2)],'Scores',[score(:,1) score(:,2)],'Varlabels',categories);

Best Answer

The biplot() function has an output that lists handles to all objects in the plot. All you need to do is isolate the handles to the scatter points by referencing the handle tags and then assign color based on the category.

If you have any questions, feel free to leave a comment.

% Your code
categories = ['F1';'F2';'F3';'F4';'F5';'F6';'F7';'F8'];
load('MAT_ALL.mat')
% figure(1)  (No need for this)
[coefforth,score,~,~,explainedVar] = pca(MaT_All(:,9:16));
load('DataGroup.mat')
clusters = DataGroup(:,20);
[coefforth,score,~,~,explainedVar] = pca(MaT_All(:,9:16));
figure()
% Store handle to biplot
h = biplot([coefforth(:,1) coefforth(:,2)],'Scores',[score(:,1) score(:,2)],'Varlabels',categories);
% Identify each handle
hID = get(h, 'tag'); 
% Isolate handles to scatter points
hPt = h(strcmp(hID,'obsmarker')); 
% Identify cluster groups
grp = findgroups(clusters);    %r2015b or later - leave comment if you need an alternative
grp(isnan(grp)) = max(grp(~isnan(grp)))+1; 
grpID = 1:max(grp); 
% assign colors and legend display name
clrMap = lines(length(unique(grp)));   % using 'lines' colormap
for i = 1:max(grp)
    set(hPt(grp==i), 'Color', clrMap(i,:), 'DisplayName', sprintf('Cluster %d', grpID(i)))
end
% add legend to identify cluster
[~, unqIdx] = unique(grp);
legend(hPt(unqIdx))

You can select a different color map (I'm using 'lines'). : https://www.mathworks.com/help/matlab/ref/colormap.html#buc3wsn-1-map 190425 094457-Figure 1.jpg

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MATLAB: Can I add 95% confidence ellipses around groups of data in a pca plot (biplot)

If you know the center of the clusters and the CI's along the x and y axes for each cluster, you can use this function to plot the ellipses

https://www.mathworks.com/matlabcentral/answers/476867-how-can-i-draw-std-ellipses-in-a-scatter-plot#answer_388409

A comment below that answer points to an alternative solution as well.

Also check the file exchange.

Addendum

The block of code below implements the ellipses outlined in the first link above with your data which is attached. I made additional changes from your version to clean some stuff up a bit.

Stars mark the center of each cluster using the mean (consider using the median instead since the data are not normally distributed). Major and minor axes of the ellipses represent the 95% CI using the percentile method which is a good method given that the data are not normally distributed.

load('data.mat')
[coeff,score,latent,tsquared,explained] = pca(X);
f1=figure(); 
h= biplot(coeff(:,1:2),'scores',score(:,1:2),'color','k','marker','.','markersize',17,'varlabels',...
    {'DO','O2sat','pH','Temp','Sal','Depth','PAR','|Velocity|'});
hold on
%color by site
hID = get(h,'tag'); %identify handle
hPt = h(strcmp(hID,'obsmarker')); %isolate handles to scatter points
[grp, grpID] = findgroups(site);
clrMap = winter(numel(grpID));
p = 95; % CI level
for i = 1:max(grpID)
    set(hPt(grp==i), 'Color', clrMap(i,:), 'DisplayName', sprintf('MSP%d', grpID(i)))
    
    % Compute centers (means)
    allX = arrayfun(@(hh)hh.XData(1), hPt(grp==i)); 
    allY = arrayfun(@(hh)hh.YData(1), hPt(grp==i)); 
    centers(1) = mean(allX);  % x mean
    centers(2) = mean(allY);  % y mean
    
    % Plot centers, do they make sense?
    plot(centers(1), centers(2), 'rp', 'MarkerFaceColor', clrMap(i,:), 'MarkerSize', 20, 'LineWidth', 1)
    
    % Compute 95% CI using percentile method
    CIx = prctile(allX, [(100-p)/2, p+(100-p)/2]); % x CI [left, right]
    CIy = prctile(allY, [(100-p)/2, p+(100-p)/2]); % y CI [lower, upper]
    CIrng(1) = CIx(2)-CIx(1); % CI range (x)
    CIrng(2) = CIy(2)-CIy(1); % CI range (y)
    
    % Draw ellipses
    llc = [CIx(1), CIy(1)]; % (x,y) lower left corners
    rectangle('Position',[llc,CIrng],'Curvature',[1,1], 'EdgeColor', clrMap(i,:));
    
end
title('Full Deployment (12h)');
set(gca,'fontsize',18)
xlabel('Component 1 (55.26%)') % how can I add percent ('%s %', explained(1))')
ylabel('Component 2 (21.87%)')
[~, unqIdx] = unique(grp);
legend(hPt(unqIdx))

MATLAB: Delimit a text file based on columns of cells

I figured out how to do it. basically, use the function

newstr = compose(str)

so I just added the newline character to the end of each of my lines, and used that.

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