Pathview parsing error

Question

[ladypurrsia]

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.

Thanks!!

[gaspilleura]

Hi, I am having thee same exact problem. Could you solve it?

thank you

Answer 1

[AK]

If you remove kegg.native = FALSE or make it TRUE you'll get the following figure (ko00195.pathview.png):

ko00195.xml and ko00195.png are template files that your data will be anchored to. Tested by:

> SP.KEGG
       log2FoldChange
K00005     -1.5503608
K00045     -0.7369513
K00150     -1.4072273
K00214     -1.3487558
K00218     -1.8065475
K02703     -0.6513490
> pathview(
   gene.data = SP.KEGG,
   species = "ko",
   pathway.id = "00195",
   gene.idtype = "KEGG"
 )
Note: Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
Note: Mapping via KEGG gene ID (not Entrez) is supported for this species,
it looks like "K01488"!
Info: Downloading xml files for ko00195, 1/1 pathways..
Info: Downloading png files for ko00195, 1/1 pathways..
Info: Working in directory
Info: Writing image file ko00195.pathview.png