I'm just learning to work with Pathview package, it sounds great, however, I had a problem with it. Hope it is solved here. I used the following command:
pv.out <- pathview(gene.data = df[,1], pathway.id = "00906", species = "ath", out.suffix = "df", kegg.native = T)
I used Entrez ID for gene ID type, the head of my "df" file is like below:
ID logFC 1 824011 10.790438 2 820667 9.013788 3 838887 9.793571 4 838504 9.715823 5 10723101 8.816703 6 830443 8.663770
Among the above gene ID, one of them is involved in the Carotenoid biosynthesis pathway (pathway Id of "00906"), but the software told "Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong". Here is the output of the above command:
Info: Getting gene ID data from KEGG...
Info: Done with data retrieval!
Info: Downloading xml files for ath00906, 1/1 pathways..
Info: Downloading png files for ath00906, 1/1 pathways..
Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory C:/Users/dps/Documents
Info: Writing image file ath00906.df.png
Also, the sessionInfo() is below:
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
 pathview_1.10.1 org.Hs.eg.db_3.2.3 RSQLite_1.0.0 DBI_0.4-1 AnnotationDbi_1.32.3 IRanges_2.4.8 S4Vectors_0.8.11
 Biobase_2.30.0 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
 KEGGgraph_1.28.0 XML_3.98-1.4 Biostrings_2.38.4 png_0.1-7 R6_2.1.2 grid_3.3.1 httr_1.2.0 graph_1.48.0 zlibbioc_1.16.0
 curl_0.9.7 XVector_0.10.0 Rgraphviz_2.14.0 tools_3.3.1 KEGGREST_1.10.1
Could you please help me out to solve the problem?