I gave a talk on graph theory using R.
One library that I used was Rgraphviz. It is available from bioconductor.
Examples from my talk.
in graph library
undirected random graph
V M g1 g1 renderGraph(g1)
This a is a list of books most of which I have previously reviewed.
Algorithms, Robert Sedwick, Kevin Wayne 2011
The Black Belt Memory Jogger, Six Sigma Academy 2002
Six Sigma with R, E. Cano, J. Moguerza, A. Redchuk 2012
Graphical Models with R, S. Hojsgaard
The Cartoon Guide to Statistics, L. Gonick & W. Smith
R for Business Analytics, A Ohri
The Art of R Programming, N Matloff
The Elements of Statistical Learning, T. Hastie, R. Tibshirani, J. Friedman