[R] Questions about 'igraph' package.......

[Gábor Csárdi]

On Mon, Mar 28, 2011 at 3:05 PM, karena <dr.jzhou at gmail.com> wrote:
> I am using 'igraph' package to make some graphs of 'gene-gene interaction'.
>
> I can get a data.frame which has three columns.
> gene1      gene2          pvalue
> AGT         MLR            1.2e-04
> MLR         11BHSD1      1.71e-05
> IFG2        11BHSD2      2.2e-07
> .             .                 .
> .             .                 .
> .             .                 .
> AGTR1     NPPA            3.2e-2
>
> I have several questions:
> 1) How can I make a plot in which the width of the edges can represent the
> significance of the epistasis p values? I am thinking about getting another
> column which is the -log(pvalue), so the larger the value is the more
> significant the p value is.

epiG <- graph.data.frame(epitab)
coords <- layout.fruchterman.reingold(epiG, weights=-log10(E(epiG)$pvalue))
plot(epiG, layout=coords, edge.width=-log10(E(epiG)$pvalue))

> 2) After I get the graph, how can I modify the image. Because all the nodes
> in the image are numbers (0,1,.....,100), how can I add the gene name to
> each node in the image?

You cannot modify the image after the plotting. Well, you can, but it
is a lot esier
to specify all the parameters at the time of the plotting:

plot(epiG, ..., vertex.label=V(epiG)$name, ...)

See ?igraph.plotting for details.

Best,
Gabor

>
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-- 
Gabor Csardi <csardi at rmki.kfki.hu>     MTA KFKI RMKI