[BioC] How to use the same node layout for a set of graph plots using graph and Rgraphviz?

Ariel Chernomoretz ariel at df.uba.ar
Sat Feb 9 19:13:23 CET 2008

Hi Hugh,

I was testing your handy code and got the following weird behavior.
For some input graphs plotGraphWithTemplate works fine with the default
layout ("dot") but
fails when "neato" is requested.
Of course this has to do more with the Rgraphviz plot call rather than with
your function ,
but I will be happy to hear your opinion (or any bioc user) about this.

'g' and 'gg' are two small graphs  I am sending you in separate email

>  require(Rgraphviz)
>  load("gdata.Rdata")
>  plotGraphWithTemplate(g,agopen(gg,"foo"))               #non hidden edges
are blue. Ok.
>  plotGraphWithTemplate(g,agopen(gg,"foo"),"neato")   #every single edge
plotted in black

> sessionInfo()
R version 2.6.1 (2007-11-26)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rgraphviz_1.16.0 graph_1.16.1

loaded via a namespace (and not attached):
[1] cluster_1.11.9  rcompgen_0.1-17 tools_2.6.1

Thanks for your help,

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