For my latest publication, I decided to generate all my images purely based on 100% Mathematica code. Images are based on real data and simulations (all processed in Mathematica as well). The figure used are directly saved from Mathematica and not touched by any other program.
Not sure if it saved time in the end. But as in any publication you have to remake the images many times, changing data or layout. That at least was easy once I had all the code for the images remaking them was very easy and fast. Making them in the first place… not so much. But I learned a lot of new tricks. And in the spirit of open science, I was able to upload my notebooks for data processing and the figure generations as supplemental files.
Regrettably in my field of research only very few people use Mathematica (mostly Matlab, and increasingly more python). But it never hold me back (mostly because porting it all to python would be to much work ;).
But, I would like to point out something: Suppose you want to include these plots in an article you are working on, with text written in TeX. Then exporting the Mathematica graphics to pdf and including them in your TeX file works fine, up until the point of text label size compared with your text produced by LaTeX.
TikZ, on the other hand, takes care of this issue, since it is a bunch of TeX macros (whereas it is probably more difficult to learn).
Mathematica graphics abilities are impressive indeed. It is a brilliant tool that I am very fond of, and if you “have to remake the images many times, changing data or layout”, then Mathematica is the thing to work with. But as I see it, up until the point of text size.
I recently, when working on my Physics M Sc thesis, found my self changing the Axes labels and ticks text size from 14 to 16 to 17 and then to 18 points, which in turn depend on the ImageSize option, just so it looks better in the pdf output.
So as I see it, the best way is to analyze your data in the Mathematica environment, and the create a similar figure with that data in TikZ.
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