[BioC] import DOT (GraphViz) into Cytoscape

[Dan Tenenbaum]

On Mon, Sep 26, 2011 at 12:14 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> 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.

It looks like Gephi can export to CSV format, and Cytoscape can read
this format. You just need to tell Cytoscape which columns contain
which information.

Dan



>
> 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
>>
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>