Creating a simplified network

[Jordan Mackay]

Hello, Cytoscape experts!

I built a network from importing physical interactions from web service and all interactions (edges) are two-way. Is there any way to simplify the network at all by collapsing all of these redundant undirected edges into a single undirected edge per pair of nodes? I would prefer finding a method of collapsing the two edges without rebuilding my network, but I couldn't find any ways to do that easily.

Your help would be greatly appreciated!

Jordan

[piet molenaar]

Hi Jordan,

Unfortunately there is no 'collapse edges' button.

Are all edges of the same type? If not you can filter them out using the filter tools.

Or can you export the data from the webservice in another format? This might enable filtering the data beforehand.

Hope this helps,

Piet

Jordan

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
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the Netherlands

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[Jordan Mackay]

Hi Piet,

Thank you for the suggestions. Something I did that turned out to work for me was using the "remove duplicated edges" in the modify networks tab under the plugins menu, ignoring edge directionality. This seemed to worked to reduce the two edges to one edge between two nodes. 

I appreciate your response!

Jordan

[piet molenaar]

Aha, nice! 

I wasn't aware of  a plugin supporting this, which plugin does this functionality belong to?

Tnx,

Piet

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[Tim Kacprowski]

hi

that functionality belongs to NetworkAnalyzer (now core plugin)

cheers

tim

____________________________________________

Tim Kacprowski

Molecular Networks in Medical Bioinformatics

Max Planck Institute for Informatics

http://www.medbioinf.de

Campus E1.4, 66123 Saarbrücken, Germany

Phone: +49-681-9325-3022

____________________________________________