Can you achieve the plot you're after when using gnuplot directly?

If not, then you should probably start by doing that; and seek out some gnuplot expertise to help; and then come back to the Perl interface later. On past experience, there's not much of that around here.

For my part, I have never worked out how to get gnuplot to do what I want. Like so many OSS packages, it probably contains really amazing code, but the documentation is such that the you need to dedicate years to working out the effects of combining its various obscure directives before you will be able to produce what you want from it rather than just having to accept what it decided to produce. It seems to be fine if all you want to produce is a pretty picture; but if you need that picture to be interpretable in the sense that real and accurate information can be read back from it, look elsewhere.