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:188.8.131.52). 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.