Venn and Euler Diagram tool in Cytoscape 3.0

[Hunter Richards]

Hi,

Is there a way to create groups in Cytoscape 3.0 so that I can generate Euler diagrams?

In Cytoscape 2.8 I can use the groupTool v1.3 to create groups and with the VennDiagramGenerator tool (v1.4) make Eulers but the elements on the graph never aligned themselves properly, and there's no way to extract the table of intersection names and areas, and number of elements.

Plus there's no way of saving/exporting the diagram like there is for Venn diagrams in heuermh's VennDiagrams (v0.5) tool. I can only take screen snips or grabs. Ugh. I'm hoping new version (v1.02) for the latest Cytoscape will work properly.

Thanks!
-hunter

[Michael Heuer]

Hello Hunter,

The Cytoscape 2.x VennDiagramGenerator (v1.4) and VennDiagrams (v0.5)
plugins were merged into the Cytoscape 3.x Venn and Euler Diagrams app

http://apps.cytoscape.org/apps/vennandeulerdiagrams

The first 10 seconds of this video demonstrate one way to create
groups, by selecting nodes, right click Group --> Group Selected
Nodes. To rename the newly created group, select the group in the
Group view, right click Rename Group... or hit ctrl/command-shift-r.

https://www.youtube.com/watch?v=EmXPVTzC6S4

michael

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[Hunter Richards]

Thanks Micheal,

I saw that tutorial. In v3.0 That requires to have all the samples grouped. In v2.8 I simply created 4 networks and used the GroupTool to put them together. From there I could use the venn/euler diagram tool. I can't find a grouping tool for 3.0. And right-selecting a network and grouping the nodes, giving the group a unique name, and the using the Venn/Euler app does not work. Only one
group show up in the Venn/Euler app selection window.

-hunter

[Hunter Richards]

No one? Am I really the only person who can't get this to work? Four separate lists -> Euler diagram. Got it to work in 2.8, but not in 3.0. None of the videos are helpful either.