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[igraph] dendogram visualization

From: Kurt J
Subject: [igraph] dendogram visualization
Date: Wed, 5 Nov 2008 15:05:22 +0000

Hi iGraphers,

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

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.

Kurt J

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