There are probably various ways to solve this. If the colors are adequate and you merely want to change their ordering, consider the example:
clc; clf;
% simple stacked bar chart
A = [3 2 5; 2 1 6; 5 8 2];
subplot(1,2,1);
bar(A, 'stacked');
subplot(1,2,2);
h=bar(A, 'stacked');
newordering=[3 2 1];
CD={h.FaceColor};
for c=1:numel(h)
h(c).FaceColor=CD{newordering(c)};
end
This gives us the result:
In this case, I reversed the color order, but you can specify any order with the variable newordering.
This works in R2019b, but not R2015b. Unless specified otherwise, I'm going to assume you are using a relatively new version.
