I have two objections to Gnuplot. First, it doesn't include a real programming
language. This means the various types of data manipulation needed to set up
most plots have to be done by an external program. Second, when gnuplot
doesn't produce exactly what you want, it is difficult or impossible to make
significant changes to the plot.
(Also worth noting is that gnuplot's barely-DFSG license has caused problems
for Debian in the past. See #100612)
For non-interactive applications (e.g. web) one can use R. Note that R's PNG
and JPEG devices rely on having an X server present. I've had success with R
producing EPS output, and then using Imagemagick's convert command, which calls
Ghostscript behind the scenes, to rasterize it.
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