[BioC] import DOT (GraphViz) into Cytoscape

[Dan Tenenbaum]

On Fri, Sep 23, 2011 at 12:24 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Dear List,
>
> I realize my question is somewhat distantly related to the use of BioC, but maybe someone faced the same challenge before: how to import a DOT file (generated using RGraphViz) into Cytoscape. This is not as straight forward as I hoped it would be... i.e. i can't get it to work.

A little googling suggests you could use this perl library to convert
your DOT file to GRAPHML format:

http://search.cpan.org/~tels/Graph-Easy/bin/graph-easy

Then use this cytoscape plugin to import GRAPHML:

http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=GraphMLReader

Dan

>
> Any thoughts are appreciated!
>
> Guido
>
>
> ---------------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl
> internet:   http://nutrigene.4t.com
> http://www.researcherid.com/rid/F-4912-2010
>
>
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