[BioC] import DOT (GraphViz) into Cytoscape

Hooiveld, Guido Guido.Hooiveld at wur.nl
Fri Sep 23 22:09:28 CEST 2011

Hi Dan,

Thanks for your prompt response; I will give it a try.
The Graph-Easy route didn't pop-up when I was searching the net. I tried to go via the dot -> gxl route, but that failed.


-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Friday, September 23, 2011 21:40
To: Hooiveld, Guido
Cc: bioconductor (bioconductor at stat.math.ethz.ch)
Subject: Re: [BioC] import DOT (GraphViz) into Cytoscape

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:


Then use this cytoscape plugin to import GRAPHML:



> 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
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> http://www.researcherid.com/rid/F-4912-2010
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