customized visualization of edges between groups in cytoscape

Question

[shangyuan5000]

Hi,

I have a complicated gene network. To make the network easier, I grouped and collapse some of the genes with similar functions in Cytoscape 3.7.

After that, the edges between that group (Group G, for example) and other genes (gene C, for example) were automatically assigned with NA in the edge table. However, I wanted the maximum or the mean value of all edge weights between gene C and genes in group G.

Does anyone know how to do that? I thought Metanodes plugin or Group Tools might have the function. However, they are not supported in the new Cytoscape versions.

Thanks & Best regards,

Raymond

Answer 1

[scooter]

Hi Raymond, What you are asking for is edge table aggregation. We've implemented it for nodes, but not yet for edges. We already have a feature request for this (https://cytoscape.atlassian.net/browse/CYTOSCAPE-11562), but it's not currently slated for a particular release.

-- scooter