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Question: import DOT (GraphViz) into Cytoscape
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gravatar for Guido Hooiveld
6.2 years ago by
Guido Hooiveld2.1k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.1k 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. 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@wur.nl internet: http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.2 years ago by Dan Tenenbaum ♦♦ 8.2k • written 6.2 years ago by Guido Hooiveld2.1k
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gravatar for Dan Tenenbaum
6.2 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
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=Gr aphMLReader 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 >
ADD COMMENTlink written 6.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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@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=Gr aphMLReader 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 >
ADD REPLYlink written 6.2 years ago by Guido Hooiveld2.1k
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@r-project.org [mailto:bioconductor- bounces@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@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=Gr aphMLReader 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
ADD REPLYlink written 6.2 years ago by Guido Hooiveld2.1k
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 > > >
ADD REPLYlink written 6.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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