MATLAB giving error while trying to create a 3D scatter plot: Error using sparse (Index exceeds array bounds)

I was following the MathWorks example: https://www.mathworks.com/help/stats/tsne.html#bvkcm24-1 which works fine for fisheriris dataset.

load fisheriris
[Y2,loss2] = tsne(meas,'Algorithm','exact','NumDimensions',3);
figure
v = double(categorical(species));
c = full(sparse(1:numel(v),v,ones(size(v)),numel(v),3));
scatter3(Y2(:,1),Y2(:,2),Y2(:,3),15,c,'filled')
title('3-D Embedding')
view(-50,8)

However, when I change a dataset to something else, it gives error:

Error using sparse
Index exceeds array bounds.

I have the following:

c = full(sparse(1:numel(v), v, ones(size(v)), numel(v), 3));
where numel(v) = 9339, size(v) = 9339 x 1 double

Here the last argument is digit '3' which I followed from MathWorks example in link above. I want to reduce it to 3 dimensions and create a 3D plot same as in that example.

In my case v has 25 classes unlike 3 in Mathworks exaple. So I changed it as follows:

c = full(sparse(1:numel(v), v, ones(size(v)), numel(v), 25));

This time there is no error in c, but I get the error below:

Error using scatter3 (line 109)
C must be a single color, a vector the same length as X, or an M-by-3 matrix.

[Walter Roberson]

scatter3(Y2(:,1),Y2(:,2),Y2(:,3),15,v,'filled');
colormap( jet(numel(unique(v))) )

[Walter Roberson]

I know your case v has 25 classes. That is why I gave the code that I gave. Though I guess you might possibly need

scatter3(Y2(:,1), Y2(:,2), Y2(:,3), 15, v(:), 'filled');
colormap( jet(numel(unique(v))) )

[Walter Roberson]

What is size(Y2) and size(v) ?

[Walter Roberson]

No, that cannot be the error, as your code is not invoking pca: your code is invoking tsne(), and tsne will return an array N x 3 where N is the number of rows in the data you are passing tsne.

[hello_world]

@Walter Roberson:

Problem resolved. I was plotting coeff which has size 512 x 512. I needed to plot score which has size 9339 x 512. I used your initial solution without considering 'c', and considering 'colormap'.

Thank you. Going to accept your answer.

[Walter Roberson]

https://www.mathworks.com/help/stats/visualize-high-dimensional-data-using-t-sne.html

[hello_world]

@Walter Roberson:

Actually, I will use this scatter3 plotting for different functions, not just tSNE. Can you please advise on the following:

(1) Is there still a way to use 'c'?

(2) Can I assign specific color to each class?

(3) How to make legend such that each color represents class name/label?

[Walter Roberson]

(1) Is there still a way to use 'c'?

No. That example only works for exactly 3 classes. The technique of using sparse like that and passing the resulting c in as the color information, works only for the case of 1 class or 3 classes.

(2) Can I assign specific color to each class

Yes. Where I showed

colormap( jet(numel(unique(v))) )

you would instead create a colormap array with as many rows as you have classes, with each row having exactly the colors you want. Then pass the v (class number) as the color data.

(3) How to make legend such that each color represents class name/label?

Use something like

hold on
for K = 1 : 25
  LH(K) = plot(nan, nan, 'Color', YourColorMap(K, :));
  LS{K} = sprintf('Class #%d\n', K);    %adjust to appropriate legend
end
hold off

and then

legend(LH, LS)

[hello_world]

@Walter Roberson:

Understand everything, but how to create colormap array to be used in question (2) & (3) above?

I am closing. If you put your reply as an answer instead of a comment, I can accept it.

[Walter Roberson]

I would prefer you did not close the question, as it might be of use to other people.

To create a colormap array, just assign to it.

mycmap = [0 0 1;
         0 0 .5;
         0 0 0;
         0 .5 0;
         0 .5 .5;
         0 .5 1;
         0 1 1;
         0.5 1 1;
         0.5 1 0.5;
         0.5 1 0;
         0.5 0.5 0;
         0.5 0 0 ];

   colormap(mycmap)

You might be interested in colormapeditor(), or in https://www.mathworks.com/matlabcentral/fileexchange/28943-color-palette-tables-cpt-for-matlab

Answer 1

[Walter Roberson]

Copying from comments:

scatter3(Y2(:,1), Y2(:,2), Y2(:,3), 15, v(:), 'filled');
colormap( jet(numel(unique(v))) )