I've enjoyed reading your blog for awhile now as I like the anthropological take on genomic data. A post back in February ( http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/1000-geno... ) was accompanied by some of the more attractive bar plots I've seen (nice alpha, great fonts) -- can you divulge what software you used?
Thanks for the kind words!
These and most of my graphs are done with Mathematica. The fonts are in the PT Sans family, which are free from Google Fonts. The color scheme is stock. I composite almost all my graphs in Illustrator and in particular add nearly all the data labels that way, even though I could do them programmatically, I find it easier to just label by hand.
This post on heritability has some xy plots also from Mathematica: