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Re: [igraph] a few questions about saving and plotting a 50k nodes netwo

From: Tamas Nepusz
Subject: Re: [igraph] a few questions about saving and plotting a 50k nodes network
Date: Wed, 10 Feb 2010 13:45:43 +0000
User-agent: Mutt/1.5.20 (2009-06-14)

Hi Yannick,

> I'm currently analysing this graph (with R) :
> [...]
> First, is it a good move to save everything as graph attributes as above ?
I don't think you'll do any harm if you do that. If it fits into the
memory of your computer, then why not.

> > plot(g.sw.gcc)
> Erreur : impossible d'allouer un vecteur de taille 261.5 Mo
> [...]
> What is wrong ? Is this graph too big ?
Probably yes. I have never tried plotting a graph of this size using R
-- chances are that you would be getting an intangible mess of edges
anyway, no matter how good the layout is. Note that it doesn't really
matter how large your graph is when you save it, as R might be
allocating several auxiliary data structures when plotting the graph
itself, and these may exceed the memory limits. I don't know how
plotting in R works and what's going on behind the scenes, but my
impression is that this simply won't work in R (or any other general
purpose graph drawing package).

Once, when I had to plot a very large graph for illustration purposes
(~70K vertices, ~500K edges), I came up with a Python script that drew
the graph itself based on a pre-calculated layout using Python's
bindings to the Cairo library.

If I were you and I really needed a visualisation of the graph, I would
try plotting the graph without the edges first. In other words, create
an empty graph with the same number of vertices and plot that, using
your precalculated DrL layout. If R fails to do that, maybe GraphViz can
(http://www.graphviz.org), but I don't know how to pass a predefined
layout to GraphViz, or whether it's even possible or not.

> Thirdly, do you have any recommendations, when using closeness.estimate or
> betweenness.estimate, in the choice of cutoffs ?
I'm not aware of such recommendations in the literature.


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