Hello BioConductor Group:

I have recently downloaded the package pathview. 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)

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

> traceback()
3: stop(stop.msg)
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!

Joany

**EDIT:

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")

[1] "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!

You may want to update your pathview and Bioconductor to the latest release version. Similar issue was report and solved a few months ago: Recent build and parsing error in pathview

you may always use pathview web server as an backup when needed:

https://pathview.uncc.edu/

HTHs.

Thank you very much! I had recently downloaded the package (only a few days), but I went ahead and did an update on all bioconductor packages. The command works now, however ;only when kegg.native = TRUE. If kegg.native = FALSE, I get the following error:

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"!
Note: ko00195 not rendered, 0 or 1 connected nodes!
Try "kegg.native=T" instead!

Is there another way to get a .pdf output instead of a .png?

Thanks!