You can use the new feature, Color Data (CData) property for bar graph released in R2017b. You can change the color for a particular bar by setting the FaceColor property to 'flat'. Then change the corresponding row in the CData matrix to the new RGB triplet. Here is the link for the CData property in bar graph: CData
For example,
a = [1,3,6;2,5,6;8,2,1];
H=bar(a, 'stacked');
colorSet = [];
for i = 1:3
myColors = round(rand(3,3),1);
colorSet = [colorSet myColors];
H(i).FaceColor = 'flat';
H(i).CData = myColors;
end
This will display the bar plot with different colors. Similarly for the different bar plot you can set the CData property of the other bar graph to the above colors.
