Dear Biostars community:
I have recently downloaded the package pathview from Bioconductor. My dataset is a matrix that looks like this:
head SP.KEGG log2FoldChange K00005 -1.5503608 K00045 -0.7369513 K00150 -1.4072273 K00214 -1.3487558 K00218 -1.8065475 K02703 -0.6513490
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)
Which produces 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!!!
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: Pathview Reference Manual 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.." 1 "Downloading png files for hsa04110, 1/1 pathways.." Parsing ./hsa04110.xml file failed, please check the file!
I have read in other websites that the package
dplyr can mask things in this package, so I have rebooted my R, and loaded pathview last. Nothing works. Any photon of light into this conundrum would be greatly appreciated.