Hi,

I saw Fig.2C (https://www.nature.com/articles/s41419-020-2477-1/figures/2) and the pathway visualized is not in the KEGG database. I asked myself how the authors created a custom KEGG pathway. They cite pathview in their methods that they used pathview for pathway visualization but I couldn't find a way to visualize custom pathways, that aren't uploaded in the KEGG database.

Any ideas or suggestions? Thank you.

It either part of a standard KEGG pathway (note the truncated graph) or a custom pathway. If it is a custom pathway, you will need to have two files: a KGML (XML) pathway definition file and a png pathway diagram, in your directory specified by kegg.dir argument in pathview() function.

Let my try to rephrase my question.

Can you change the visual KEGG pathways and use the changed version as an input for visualizing gene expession changes similar to the output of the pathview package? Or can you use a selfmade pathway cartoon as an input for visualizing gene expession changes (with pathview or a comparable package)?

Thanks!