Hi,

I'm trying to use the Pathview package to highlight ECs based on a KEGG module. For example, I'd like to highlight module M00039 in pathway map00940 (i.e., Phenylpropanoid Biosynthesis). In pathview, I'm using the "ko" species. Also, I know how to extract the KOs for given a module (i.e., keggLink("module","ko")), but this involve KOs outside the module of interest for instance K00487 (mapped to EC:1.14.13.11). My ultimate goal is to include gene expression data for the highlighted KO.

pv.out <- pathview(gene.data = "K00487",
                   pathway.id = "00940", out.suffix = "toy.example", species = 'ko')

Would be possible in somehow to highlight just the ECs within a module?

I will appreciate any suggestion.

Regards,

William

You can definitely visualize/highlight just ECs/genes/nodes from a particular module. In you case, you can do something like:

library(pathview)

library(KEGGREST)

m1=keggLink("ko","M00039")

m1=gsub("ko:", "", m1)

pv.out <- pathview(gene.data = m1, pathway.id = "00940", out.suffix = "toy.example", species = 'ko')