(Thanks Marc for referring to KEGGgraph)

Hi Daniel,

   In case of visualizing KEGG pathways, 'KEGGgraphApp' vignette in the
KEGGgraph package gives two examples. In principle one could draw the graph
object acquired from KEGG via KEGGgraph package with Rgrapvhiz package.

  A toy code snippet:

library(KEGGgraph); library(Rgraphviz)
>
somegraph <- parseKKGML2Graph(xmlFile)

pdf("filename.pdf")
>
plot(somegraph, "neato")
>
dev.off()
>

>

  In the KEGGgraph package there are several files attached as examples, you
could try to use them as a starting point. Currently the KGML files on KEGG
database webserver are not consistent and I believe the staffs are working
on it (see the other email in the mailing list titled 'KEGGgraph, error'), I
will post then when the KGML files are functional again.

  In case of questions please do not hestitate to ask me.

  Best wishes,
David
2009/4/16 Daniel Brewer <daniel.brewer@icr.ac.uk>

> Hello,
>
> >From a couple of interesting gene lists I have found KEGG pathways which
> contain genes from both lists.  Does anyone know how to visualise this?
>  I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different colours.
>
> I can cope with this not being done in bioconductor but would prefer it
> if the final image was exported as PDF.  I have searched around without
> much luck ... it seems possible that KEGGgraph maybe able to do it but
> it is not clear from vignette.
>
> Dan
>
> --
> **************************************************************
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> Email: daniel.brewer@icr.ac.uk
> **************************************************************
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