![]() png of the general photosynthesis pathway, but all protein boxes underneath the picture are one color and there is no scale. The first is an empty file the second, just a. When I do run this command, 2 files pop up in my working directory: 1) ko00195.xml 2) ko00195.png. *Funny thing, I checked, and K01488 is in my row!!! ko00195.xml file failed, please check the file! Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"! Parsing. pathview(gene.data = SP.KEGG, species = "ko", pathway.id = "00195", gene.idtype = "KEGG", kegg.native = FALSE) I am running the command in R studio like this - I am wanting to see the general Photosynthesis KEGG reference pathway. After reading the manual, I don't see why I should not be able to map to a certain reference pathway with this data-set. ![]() I don't have a specific organism I am working with as these are results from environmental samples (shotgun metagenomic, Illumina sequencing) and thus it contains thousands of species. Where row.names (> 300 total unique entries) are KO numbers and the only column is the log2-fold change (previous analysis). My dataset is a matrix that looks like this: head SP.KEGG I have recently downloaded the package pathview from Bioconductor.
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