William Longabaugh's BioFabric gives us a powerful new visualization technique for large networks. He has implemented BioFabric fully in Java and partially in R and d3.js.
Longabaugh, W.J.R. [Combing the hairball with BioFabric: a new approach for visualization of large networks](http://www.biomedcentral.com/1471-2105/13/275). BMC Bioinformatics, 13:275, 2012.
I hope to have an R htmlwidget with BioFabric for this week's Building Widgets widget of the week. It is very, very early, but I'd love feedback at https://github.com/timelyportfolio/RBioFabric.