R has several systems for producing complex plots.  Two of the more sophisticated are lattice and ggplot2.  Lattice is documented in Deepayan Sarkar’s book Lattice: Multivariate Data Visualization with R; ggplot2 is based on the the concepts presented in The Grammar of Graphics and is documented in Hadley Wickham’s book ggplot2: Elegant Graphics for Data Analysis.

There is an excellent series of posts on the LearnR blogsite that compares Lattice and ggplot2 by reproducing the plots from the lattice book using ggplot.  This is an excellent resource for learning both ggplot and lattice.