[BioC] Drawing network graphs (i.e. nodes and edges)
Peter
bioconductor-mailinglist at maubp.freeserve.co.uk
Thu Feb 2 16:57:35 CET 2006
Does anyone know of any existing R (r-project) code/library/package for
drawing graphs - the network variety consisting of nodes and edges (or
points and lines/arrows)?
e.g. Genes and interactions
For example, I might have a list of three edges for four genes:
Gene1 -> Gene2
Gene2 -> Gene3
Gene4 -> Gene3
Which would give the following simple graph:
Gene1 -> Gene2 -> Gene3 <- Gene4
Or perhaps as a matrix, which for four genes would be 4 by 4:
[ 0 1 0 0 ]
[ 0 0 1 0 ]
[ 0 0 0 0 ]
[ 0 0 1 0 ]
Here I have used the "rows" as the "from" and the columns as the "to"
connections.
I was hoping there was an existing library that would accept this sort
of network definition and draw a picture of it. Maybe labelled circles
for the nodes (genes) with arrows for the edges (interactions).
The hard part of this is the spatial layout of the nodes to avoid the
edges intersecting unrelated nodes. One simple answer is to draw the
nodes equally spaces on a large circle. Apart from the special case of
self interactions, all the edges would be inside the circle and thus
never cross another node.
e.g. This sort of image:
http://www.cs.toronto.edu/~wayne/research/ramsey/r.3.9.35.gif
Of course there is the extra gloss of being able to draw a connection
weight using line thickness etc.
Any ideas? I haven't found anything on Google...
Thank you
Peter
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