Hi Ariel,

There is a known issue with the code I wrote (which I discovered last week). The problem arises because an edge from node "a" to node "b" can be named in two ways: "a~b" or
"b~a". I thought this would be easy enough to get around by using the 'recipEdges' argument to 'edgeNames', but I am still working on it (There seems to be a lack of understanding on my part about how the different graph classes work.). It is also clear that the code needs modifications to properly handle directed graphs. Fixing this is also underway.

I have not tried anything other than the "dot" layout, but I would not be surprised if fixing the above problems helps with "neato".

I did not get the 'g' and 'gg' graphs - can you try sending them again?

Hugh

p.s. I am out Wed-Fri, so I won't have much time until next week to work on this.

________________________________
From: algo107@gmail.com [mailto:algo107@gmail.com] On Behalf Of Ariel Chernomoretz
Sent: Saturday, February 09, 2008 10:13 AM
To: bioconductor@stat.math.ethz.ch; Rand, Hugh
Subject: Re: [BioC] How to use the same node layout for a set of graph plots using graph and Rgraphviz?

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)
i386-redhat-linux-gnu

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,
Ariel./

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