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Comment by amelius | Hacker News Reader

In that case, I'd recommend structuring your scripts such that you can easily rerun them later on (e.g. using a Makefile). That has also other advantages, such as the ability to change graph colors, axes, or even data.

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I'm a big fan of being able to generate a document and know that the results are all based on the same, latest data and the same code. The more different things I have to do to generate it all from scratch the more likely there's something I'll forget when I have just fixed a problem somewhere.

This is what I do, really. Regarding styling I have a small styling script that I put after each graph. This small script takes the active figure (gcf) whatever it is, and changes it to my liking. So if I want to change the graph styling at a later stage I modify this small script and then re-run the main file.

But everything in MATLAB, then I just symlink the pdf figures to the manuscript folder, so with an F5 in MATLAB and a build in Sublime I have the manuscript updated.

My only problem with doing everything in Matlab (which I used to do) and exporting the PDF is that you can't really match the fonts easily to the main document. I picked a set of fonts (math and normal) for my Ph.D. thesis and I wanted the fonts in the figures to match those in the main body. Using matlab2tikz did that for me.

You could probably do the same thing but do the export of the tikz file instead of the PDF. That's basically what I do.

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