Some great general advice here, but regarding a specific point:
> An illustration software: I personally prefer Inkscape, but the industry standard Adobe Illustrator or newcomer Sketch are just as good. Use it to post-process your plots and graphs; it’s often much easier than writing plotting directives in Matlab or matplotlib.
This is something I've been grappling with for a while. It's true that plotting directives are an awful pain, especially when hopping between different graphing options for different specific problems, but on the other hand they do make re-producing the graph when you have new data wonderfully straight-forward. I still don't know what the best workflow is here.
The best candidate seemed to be Sweave+ggplot, but it's very slow to produce complicated graphs, and certain kinds of data manipulation in R aren't as easy as in Matplotlib/SciPy, so I'm going back to IPython notebooks now. But I really haven't found a great solution.
As an aside, there's a good GUI/scriptable graphing app for OS X that just had a major update here: http://plot.micw.eu It's a bit quirky, but it definitely fills a niche.
> An illustration software: I personally prefer Inkscape, but the industry standard Adobe Illustrator or newcomer Sketch are just as good. Use it to post-process your plots and graphs; it’s often much easier than writing plotting directives in Matlab or matplotlib.
This is something I've been grappling with for a while. It's true that plotting directives are an awful pain, especially when hopping between different graphing options for different specific problems, but on the other hand they do make re-producing the graph when you have new data wonderfully straight-forward. I still don't know what the best workflow is here.
The best candidate seemed to be Sweave+ggplot, but it's very slow to produce complicated graphs, and certain kinds of data manipulation in R aren't as easy as in Matplotlib/SciPy, so I'm going back to IPython notebooks now. But I really haven't found a great solution.
As an aside, there's a good GUI/scriptable graphing app for OS X that just had a major update here: http://plot.micw.eu It's a bit quirky, but it definitely fills a niche.