You are asking for what is essentially a high level flow chart, produced automatically from existing MATLAB code, that shows how functions are called, the interactions of if statements, etc.
Unfortunately, there is no such automatic tool, and writing one would be a bit of a headache, certainly so for some codes if the author was determined to write bad code. For example, suppose I wrote code that used eval to create the name of a function and then call it on the fly? UGH. Yes, that would be an obscenity, but I probably know someone who would write that way.
Perhaps you might be able to use the profiler tool as something in the right direction. It would require you to run the code, fully exercising the various pathways that could be taken in the code. But if you could do that, then you would probably already know enough about the code that you would not need the required flow chart.
