Importing graph into Cytoscape from R igraph package

[Madhurima B]

Hello All,

I have used igraph pachake of R to form few graphs. They have edge attributes like width, colour and node attributes like label. I want to import these graphs to Cytoscape for further processing.

I have tried exporting the graphs from R in gml and graphml formats. But when I import them in Cytoscape, the edge attributes are not seen. The gml format seems to support label of the nodes but not the edge attributes. 

Can someone please help me in this regard.

Any pointers would help.

Regards,

Madhurima

[Jan Bot]

Hi,

have you taken a look at the RCytoscape package?

Cheers,

Jan

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[Paul Shannon]

RCytoscape does indeed aim to help out with tasks just like this.

Jan -- whose CytoscapeRPC plugin is the essential for RCytoscape -- pointed you towards the Bioconductor release version of RCytoscape. In the intervening six months, we have added a ton of new commands, uncountable unit tests, a few bug fixes, more examples and some 'cookbook recipes'. All of which will be officially released in mid-April -- Bioconductor has a pretty strict 6-month cycle. I can give you a pre-release copy if that would help.

We are eager to see RCytoscape put to good use. Don't hesitate to write if you encounter any difficulty.

- Paul

[Keiichiro Ono]

There are two ways to import data to Cytoscape from R.

1. RCytoscape - provides direct access to Cytoscape data models from R console.

2. GraphML reader - igraph has an option to export graph topology and
its attributes in GraphML format. You can import this file by using
this plugin:

http://code.google.com/p/graphmlreader/

Kei

2011/3/22 Madhurima B <how.man...@gmail.com>:

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