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cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
MIT License
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creation of networks using createNetworkFromIgraph() #166

Closed peranti closed 2 years ago

peranti commented 2 years ago

Hello,

Thanks a lot for this handy package.

I have a STRING network of 12,086 vertices and 249,980 edges as igraph object. Based on the previous experience with RCy3::createNetworkFromIgraph(), I tried to use the same approach. However, the network in Cytoscape is yet to be generated even after 12+ hours.

Is it advisable to use createNetworkFromIgraph() for this large size graph? What is the best approach to use to create networks of different node sizes (e.g: 500, 5000, 10000, 15000, ...)?

AlexanderPico commented 2 years ago

Sorry for the late response. That's a big one for the automation package! You are blazing a new trail. I don't know of anyone else working with such networks using RCy3, so I don't have any particular advice to give. You are figuring out the limits of size and time per your machine. That's the only way to do it.

The only tip I could give would be to set all the delays to zero as they may be introducing pauses that are not needed. Can only tell by trial and error.

    setCatchupFilterSecs(0)
    setModelPropagationSecs(0)
    setCatchupNetworkSecs(0)