KEGG graph not completely connected

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7.6 years ago

saamar.rajput ▴ 70

Hello Everyone,

I am working with KGML files, generating adjacency matrix out of it and then re-visualizing it as per my needs using igraph. But unfortunately the graph is not complete connected like it shows in KEGG itself. there are three sub graphs which are not connected to each other but should be. Any suggestion for a function that shows one completely connected KEGG graph?

igraph R KEGG • 1.8k views

ADD COMMENT • link updated 7.5 years ago by Biostar 20 • written 7.6 years ago by saamar.rajput ▴ 70

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Can you provide more detailed information on how you obtained the graph? For example, which organism do you work with? Depending on your pre-processing, several reasons are possible.

ADD REPLY • link 7.5 years ago by Manuel Landesfeind ★ 1.4k

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I am working on Homosapiens pathways especially Salmonella infection. It is not a completely connected graph.

ADD REPLY • link 7.5 years ago by saamar.rajput ▴ 70

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How did you obtained the graph? Did you put together all information from several KGML files? Are you working with signaling pathways or metabolic pathways? Can you provide an example of a reaction/connection in a KEGG pathway that is missing in your data?

ADD REPLY • link 7.5 years ago by Manuel Landesfeind ★ 1.4k

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