(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)
Some of the best figure design ideas come from cartographers. If you've ever read a Tufte book you've seen lots of examples. Let's talk about using color effectively. Penn State geography professor Cindy Brewer's ColorBrewer tool for selecting color schemes for figures has been conveniently packaged into an R library called RColorBrewer. You'll have to read up on the RColorBrewer documentation
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).