Changing Node Colors (KGML and KEGGParser)

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Adrian Quintana

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Sep 21, 2016, 1:33:28 PM9/21/16

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I am working on visualizing pathways from KEGG via downloading the KGML files and then opening them in Cytoscape 3.4 via the the KEGGParser app. I would like to edit the colors of the nodes; however, I have noticed that using a bypass will only apply the color change superficially and not actually edit the table that the data is coming from-- which is problematic when merging the networks since the color change is not carried over.

Is there any way to edit the colors on the table in a faster way than it is now (one-by-one)? I have been successful in changing them by simply changing the RGB number ID but cannot do this efficiently on the 100s of nodes I already have to edit.

Scooter Morris

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Sep 22, 2016, 10:51:58 AM9/22/16

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Hi Adrian,
Well, not sure how many different colors you have, but you could use the same technique as you do with the bypass:

Select the nodes you want to change the color of. Only these nodes will appear in the node table.
Change the RGB value of the first node in the node table.
Right click on that value and then select "Apply to selected nodes". That will apply the value in the cell to all of the currently selected nodes.