Especially when you have such pretty defaults in things like Matlab and Mathematica.
Matplotlib (http://matplotlib.sourceforge.net/) is actually the best opensource library for creating great looking graphs that I have come across, and is comparable to Matlab and Mathematica.
I guess taste comes in place - I find producing good (as in academic publication good) figures in matlab an exercice of pain. The subplot mechanism is awful (at least was 5 years ago), and it is hard to control the layout. I heard mathematic is much better in that regard, but never used it myself.
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I have used R/ggplot for a long time now, and it's exceedingly difficult to produce beautiful visualizations.
The only thing that makes tufte-quality visualizations in my experience is hand-building your graphs in tikz.
The graphs you linked to are hideous from an aesthetics point of view; font's are ugly, data:ink ratio far too low, color choices poor etc.
Especially when you have such pretty defaults in things like Matlab and Mathematica.
Matplotlib (http://matplotlib.sourceforge.net/) is actually the best opensource library for creating great looking graphs that I have come across, and is comparable to Matlab and Mathematica.
I've looked at matplotlib but still think it's ugly by default.
Compare to:
http://www.texample.net/tikz/examples/weather-stations-data/
http://www.texample.net/tikz/examples/rna-codons-table/
The beauty of tex font's + vector graphics is impressive. Try zooming in on the sparklines in the first example
I guess taste comes in place - I find producing good (as in academic publication good) figures in matlab an exercice of pain. The subplot mechanism is awful (at least was 5 years ago), and it is hard to control the layout. I heard mathematic is much better in that regard, but never used it myself.