I'm revisiting some work I've done a while ago and I want to create some visualizations of a community structure dendogram. Specifically, i'm using python and applied community_fastgreedy and community_walktrap to a network w/ just under 20k nodes.
running in the interpreter:
>>> GM.vcG.summary.__doc__
'Draws the dendrogram of the hierarchical clustering in a string'
>>> GM.vcG.summary() Python(7152,0xa000d000) malloc: *** vm_allocate(size=417792) failed (error code=3) Python(7152,0xa000d000) malloc: *** error: can't allocate region
Python(7152,0xa000d000) malloc: *** set a breakpoint in szone_error to debug Traceback (most recent call last): File "<stdin>", line 1, in <module> File "build/bdist.macosx-10.3-fat/egg/igraph/clustering.py", line 460, in summary
MemoryError
Ahh malloc my old friend. I know there is the option to change ARPACK options and this might help. But I was keen to get something a bit sexier than an ascii based dendrogram drawing anyway ;)
So let me distill this meandering post:
1 - are there any resources or examples for creating a nice dendrogram viz from an igraph VertexClustering object?
2 - does it really make sense to draw a dendrogram from a fastgreedy community structure? unless i misunderstand, the process is agglomerative and terminates before finding one large community. so the dendrogram would be sort of disconnected. however for walk_trap, the entire dendrogram is created and then the best partition selected.