[BioC] import DOT (GraphViz) into Cytoscape

[Hooiveld, Guido]

Posting again, for the archive:

Converting the DOT into GRAPHML format goes fine with the Graph Easy collection of PERL scripts.
"graph-easy testnet.dot --graphml > test.graphml"

After installing the Cytoscape plugin, the resulting GRAPHML file can indeed be imported. Unfortunately, as of yet the plugin doesn't support 'nested networks', which means that import of directed edges are not supported (and my GraphViz network is directed...]. In other words, in Cytoscape all nodes are connected through undirected edges. Taken together, this DOT -> GRAPHML -> Cytoscape route is not suitable for directed networks.

I also found (another) visual platform, called Gephi [http://gephi.org/]. The main advantage of Gephi is that it natively supports DOT files (and also GRAPHML), so there no need anymore for the before-mentioned conversion route. IMO the main disadvantage is that Gephi is yet less well developed compared to Cytoscape, and you will have to learn (again) how to use a new program.

Guido

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Hooiveld, Guido
Sent: Friday, September 23, 2011 22:09
To: 'Dan Tenenbaum'
Cc: bioconductor (bioconductor at stat.math.ethz.ch)
Subject: Re: [BioC] import DOT (GraphViz) into Cytoscape

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.

Guido

-----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:

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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