In the early 1990's I made heavy use of a program called GLE written by Chris Pugmire of CSIRO. It was capable of producing very complex, (or simple), high quality publication ready graphs. I hadn't heard of Perl at that stage, but I was able to do some scripting of it using DCL on Vaxes. Doing something similar in Perl should be easy enough. At present it runs on Linux and Windows machines.

I highly reccomend this package. I now use R all day long, and i love it dearly (though not as much as Perl). I think that GLE was a better package than R for publciation quality graphics

Have a look here for the Linux version and over here for the Windows version. Let me know how you get on!