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

[Saurin D. Jani]

Hi Peter,

You can try http://graphexploration.cond.org/  which allows interface to R and
its cool software with all lines, arrows, nodes etc, and you can do
GeneOntology lay out and Query...as well......!!

Howmany genes (neurotrnsmitter TAG Domain) --> interacts with --> endocytosis
TAG Domain

may be better than cytoscape..!! ( not sure )

Saurin

-- 
|------------------------------------------------
| Saurin D. Jani,MS
| Statistical and Research Analyst
|
| Department of Cell Biology and Anatomy
| Medical  University of South Carolina (MUSC)
| 173 Ashley Ave
| Charleston,SC - 29407
|
| Email: jani at musc.edu
| Phone: (843)792-1340
| Website: http://www.musc.edu/~jani
|------------------------------------------------


Quoting Peter <bioconductor-mailinglist at maubp.freeserve.co.uk>:

> 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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