Some pathway , carbon metabolism, ko01200, can not be plotted with fold change data

[liuxianghui]

Dear Yu: I am surprised to find that some pathway, eg carbon metabolism ko01200, can not be plotted with fold change data. It just give a n empty default pathway. However, other pathways are ok. Please kindly suggest, the following is the command and output: pathview(gene.data = names(geneList2), gene.idtype="kegg", pathway.id = "pfl01200",species= "pfl",limit = list(gene=c(min(geneList2),max(geneList2)), cpd=1)) Note: Mapping via KEGG gene ID (not Entrez) is supported for this species, it looks like "PFL_4445"! Info: Working in directory /Users/liuxianghui/work/biofilm3species Info: Writing image file pfl01200.pathview.png Info: some node width is different from others, and hence adjusted!

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