Tikz (a set of packages for latex) [1] is an excellent tool for programmatically creating figures. I drew half the illustrations during my phd using Tikz. Even

Tikz (a set of packages for latex) [1] is an excellent tool for programmatically creating figures. I drew half the illustrations during my phd using Tikz. Even if other tools are more powerful, tikz has roughly the same syntax as latex and so there is less to learn. Its a lot of easier to control the flow of the figures in a document if they are drawn using tikz because you can resize or realign them on the fly. [1] Some examples here http://www.texample.net/tikz/examples/ http://www.texample.net/tikz/examples/