By graph here I mean something resembling these images:
The ideal solution would:
I'm also interested in hearing about projects that could potentially be used as the starting point for this kind of work. If it requires some development to achieve what I want, then I'm prepared to tackle it. The most complex portion of this goal seems to be obtaining the graph layout in a reasonable time frame.
Graph# is also another option. I haven't used it personally, but I've been meaning to get around to looking over it.