In order to figure out how that code works I'd suggest first adding a pause(1) before the end of the for loop. This way you can see what happens in each loop.
Next, create your own color matrix. it creates 3 3x3 random matrices so you need to create a 3x3x3 matrix and go through them.
myColors(:,:,1) = [.2 .3 .4; .5 .5 .5; 0 0 1];
myColors(:,:,2) = ...
From what I found going through it, each loop is another section of the bar starting from the bottom. Each column are the variables in [0,1] signifying percentages for RGB. Then each row is a different stacked bar.
So for your situation you would actually need a 5x3x5 matrix looping 5 times. In an example where the middle bar has the first two sections switched to could create the matrix as follows to switch the colors.
myColors(:,:,1) = [0 0 1; 0 1 0; 0 0 1];
myColors(:,:,2) = [0 1 0; 0 0 1; 0 1 0];
