The CoMut plot from the
Broad Institute is the gold standard for representing mutational data in cancer genome studies.
The problem is that few non-computational people know how to produce a plot like this, and even
computational people have a hard time using it when the tool’s not publically available.
you also get some nice tools unavailable in R: interactive tooltips, SVG representation, etc.
As I'm more using this as a proof-of-concept, I haven't taken the time to make it sortable by
different attributes (sample, mutation abundance, etc) but all of this is possible in D3.
If you'd like to see the source, it's all in the html, just right click and select 'view source'.