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!
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!
Comment