How to select connected components in Cytoscape v 3.8.0?
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9 months ago
Ostad • 0

I am using Cytoscape v3.8.0. I am having trouble to extract connected components from a merged network. In previous versions, it could be done from tools> network analyzer> subnetwork creation> extract connected components. But in the latest version, I couldn't find that option. I went to tools> analyze network. Then there is a popup saying "Analyze a directed graph?". When I select yes, I get an overall statistics of the network. But I could not find any option to select a connected component.

cytoscape • 599 views
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9 months ago
scooter ▴ 450

Ugh. Yes, that got forgotten when the new analyzer was written. You can do the same thing with clusterMaker. Do an Apps->clusterMaker->Connected components cluster. That will add a column called "__ccCluster" that contains the component number of each connected component.

-- scooter

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Thank you very much. I will give it a go.

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Did this work for you? If I run Tools > Analyze Network I get 17 connected components, which is correct. However if I run [Apps->clusterMaker->Connected components cluster] it adds a column "__ccCluster" however all the cluster numbers are "1".

Thank you.

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