Problem: Horrible slowdowns when using scatter() in a script that you want to publish Solution: Don't use scatter. Use plot(x,y,'.') instead.
Problem: Horrible slowdown when publishing a document that has many figures in it. Symptom: You will see MATLAB cycling through all open figures. This means that it does something like this:
make fig 1
make fig 2
bring fig 1 to front
bring fig 2 to front
make fig 3
bring fig 1 to front...
...and so on.
You can see why this can become a problem.
The solution: Insert the following code after every time you're done with a figure:
snapnow();
delete(gcf);
And this really makes publish
much faster