R help - Mar 2011 - Questions about 'igraph' package.......

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. 

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?
 

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One more question is:

when you plot the gene network, you only get a number on each node, then how
can you match the numbers to the genes?

thank you very much,

Karena

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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