Can't speak for Nature but here are a few workflows I'm aware of:
- Recreate the chart using Illustrator's chart tool. Hard work, and frustrating because Adobe haven't updated the chart tool since the bronze age, but not a bad investment in time if lots of very similar charts are needed based on a similar style. It's capable of more than it looks.
- Use Illustrator to style a chart pasted in from Excel or whatever the researchers used - most statistical packages can export as
.epsor.svg- then style the vectors and change the text to fit the house style. (beware that removing the clipping masks that come with Excel charts sometimes makes lines and data points move slightly). - Trace the chart - plonk it in as an image and redraw it over the lines, then style in Illustrator. I've never needed to do this, but I've heard it's a common necessary evil in academic publishing.
- Use a code-based charting / layout tool like LaTeX or R with the ggplot2 plugin. I don't know much about this approach but it's popular with analytically and not visually minded people, is capable of professional looking results if you're patient, and the results are very consistent since it's setting up a code-based template. Here's an article with some examples using this approach - Style your R charts like the Economist, Tableau ... or XKCD
- Code up a web-based chart in something like D3, then extract the SVG output from a web browser, then open this in Illustrator and finish it for print there. The New York Times do this sometimes, I discussed this and how to get exact CMYK colours in this other question.
- Use a custom charting / visualisation tool. A popular option is Tableau which can produce very professional-looking charts plus some pretty sophisticated data vis. It's expensive, though, unless all your data is freely publicly available in which case you can use Tableau Public which is free. Quite a few scientific publications use Tableau (can't think of names of the top of my head). WEAVE is an open source alternative but nowhere near as pretty (not sure what it outputs either, but if it's SVG then Illustrator can edit it), bit more on that sort of thing here.
