KEGG graph not completely connected

Question

[saamar.rajput]

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?

[Manuel Landesfeind]

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.

[saamar.rajput]

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

[Manuel Landesfeind]

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?