I have never done this before but i suspect there must be an easy way to convert KEGG ids to pathways in R. I have a dataframe containing info from 1000 sth bacterial genomes; their taxonomy, their orfs and the kegg ids (which i identified with eggNOG functional annotation) and I would like using these ids to produce figures of pathways. Ideally I d like to have the different taxa with different colors (e.g. for carbon metabolism Firmicutes enzymes presence could be represented with red arrows, Actinobacteria enzymes presence with brown arrows etc etc) Does anyone know or have any recommendations for an R software that would easily do that? I saw KEGGprofile and I dont think it can do exactly what I am looking for - or maybe should i give it another go?
Thanks for any recommendations in advance P