[BioC] Drawing network graphs (i.e. nodes and edges)

[Sean Davis]

Look at Rgraphviz in bioconductor--it does just this.

Sean

On 2/2/06 10:57 AM, "Peter" <bioconductor-mailinglist at maubp.freeserve.co.uk>
wrote:

> 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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