Hello BioConductor Group:
I have recently downloaded the package pathview. My dataset is a matrix that looks like this:
> head SP.KEGG
Where row.names (> 300 total unique entries) are KO numbers and the only column is the log2-fold change (previous analysis). 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. 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 am running the command in R studio like this - I am wanting to see the general Photosynthesis KEGG reference pathway.
> pathview(gene.data = SP.KEGG, species = "ko", pathway.id = "00195", gene.idtype = "KEGG", kegg.native = FALSE)
And I get the following Error:
Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
Parsing ./ko00195.xml file failed, please check the file!
*Funny thing, I checked, and K01488 is in my row!!!
Here is my traceback() that I ran right after I received the error code
2: kegg.species.code(species, na.rm = T, code.only = FALSE)
1: pathview(gene.data = SP.KEGG, species = "reference",
pathway.id = "00195", gene.idtype = "ko", kegg.native = FALSE)
Here is the output of my sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Any help would be greatly appreciated in solving this perplexing result. Thank-you very much!
I thought I would note that when I do run this command, 2 files pop up in my working directory: 1) ko00195.xml 2) ko00195.png. The first is an empty file; the second, just a .png of the general photosynthesis pathway, but all protein boxes underneath the picture are one color and there is no scale.
Lastly, the examples in the reference manual (http://bioconductor.org/packages/release/bioc/html/pathview.html) are also not working. I used this command that was on page 1, under the "Quick start with demo data" section and it also gives me the same error:
pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = "04110", species = "hsa", out.suffix = "gse16873")
 "Downloading xml files for hsa04110, 1/1 pathways.."
 "Downloading png files for hsa04110, 1/1 pathways.."
Parsing ./hsa04110.xml file failed, please check the file!