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Old 12-15-2016, 02:14 AM   #1
sbcn
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Default pathview failing on metabolic pathways

Dear all,

I am using R package "pathview" to map my data to B.cereus (bce) KEGG networks.

It works very well with most networks, but I can make it work with the metabolic pathways, for example, bce01100.
I want to obtain something as Figure 5 from: http://pathview.r-forge.r-project.org/

I don't get any error message: it takes a long time to process, and at the end I get a graph with no node coloured (although I know there are genes corresponding to some of those).

My command is:
mypath <- pathview(gene.data = mygenes, pathway.id = "01100", species = "bce", gene.idtype="KEGG", kegg.native=T, split.group=F, same.layer=F)

Do these pathways work with compound data only, and not gene IDs?
In this case, how can I obtain the corresponding compound ID?

head(rownames(allsubset))
[1] "BC_r01" "BC_r03" "BC0014" "BC0018" "BC0030" "BC0044"

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.5 (Carbon)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] KEGGgraph_1.28.0 pathview_1.10.1 org.Hs.eg.db_3.2.3
[4] RSQLite_1.1-1 AnnotationDbi_1.32.3 IRanges_2.4.8
[7] S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1
[10] limma_3.26.9

loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 XML_3.98-1.5 Biostrings_2.38.4 png_0.1-7
[5] digest_0.6.10 R6_2.2.0 grid_3.3.0 DBI_0.5-1
[9] httr_1.2.1 graph_1.48.0 zlibbioc_1.16.0 XVector_0.10.0
[13] Rgraphviz_2.14.0 tools_3.3.0 memoise_1.0.0 KEGGREST_1.10.1

Thanks!
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Old 12-15-2016, 06:12 AM   #2
mastal
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I have been using pathview together with the R package 'gage'. I was working with various mammalian genomes, and I found that it would only work with Entrez Gene IDs.
I'm sure for metabolic pathways it will work with gene IDs. I'm not familiar with bacterial gene IDs, maybe the IDs you have are Entrez Gene IDs rather than kegg IDs?
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Old 12-20-2016, 04:27 AM   #3
bigmw
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sbcn,
There are a few general pathways in KEGG, like 01100, 01200 etc. they are not really classical pathways. Gene/protein nodes on these diagrams are edges instead of nodes, for example:
http://www.genome.jp/kegg-bin/show_pathway?ko01200

This is the reason why pathview does not map gene data onto these pathway graphs. Pathview does map compound data onto these pathway graphs though, as shown in Figure 5 at http://pathview.r-forge.r-project.org/.
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Old 12-20-2016, 05:19 AM   #4
sbcn
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Thank you both for your replies.
So it there a way that I can convert or reduce the data from genes to compounds? I am not very familiar with this...
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Old 12-22-2016, 06:40 PM   #5
bigmw
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Compound data and gene data are two different types, and are represented differently in pathway graphs. they cannot convert to each other.
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