[BioC] pathview -- ID Problem?

Luo Weijun luo_weijun at yahoo.com
Fri Oct 18 20:53:45 CEST 2013

Dear Fabian,
You need to update your pathview to the latest release version, which is 1.2.0. It is at:
This current release version includes all recent update features, like multiple samples/time series in one graph, and handling of all KEGG species.Your version is pathview_1.1.4, which doesn’t really handle many minor KEGG species. To ensure smooth installation, I would suggest you update your R/Bioconductor to the latest version too. Of course, you may always download and install pathview_1.2.0 manually from the link above.

BTW, for you data, you need to specify id.type="kegg" with pathview. 
pv.out <- pathview(gene.data = data_bac_values, pathway.id = "05132", species = "sey", id.type="kegg", out.suffix = "test", kegg.native = T, same.layer = F)
Read subsection 7.5 Working with species in the new vignette for more details.


 Subject: pathview -- ID Problem?
 To: bioconductor at r-project.org, fabian at tbi.univie.ac.at

 Date: Friday, October 18, 2013, 1:46 PM

 Hello Mr. Weijun Luo

 I started to use pathview to visualize my differential gene
 expressin analysis. It is really a great help. First I
 worked with human data and had no problem at all to make it

 Meanwhile I apply bacterial data and do not succeed. I'm not
 sure why. Here is my problem

 When I run the analysis with my input

 SL1344_0001 SL1344_0002 SL1344_0003 SL1344_0004 SL1344_0005
   0.1329739   0.4947647 
 -1.4013626   0.5086116  -4.0000000 

 with the following command:

 > pv.out <- pathview(gene.data = data_bac_values,
 pathway.id = "05132", species = "sey", out.suffix = "test",
 kegg.native = T, same.layer = F)
 Error in mol.data[as.character(items[hit]), ] : subscript
 out of bounds
 In addition: Warning messages:
 1: In node.map(gene.data, node.data, node.types =
 gene.node.type, node.sum = node.sum) :
   NAs introduced by coercion
 2: In FUN(1:27[[1L]], ...) : NAs introduced by coercion

 This is the error thrown out. traceback() informs like

 > traceback()
 7: cbind(mol.data[as.character(items[hit]), ])
 6: apply(cbind(mol.data[as.character(items[hit]), ]), 2,
        na.rm = T)
 5: FUN(1:27[[1L]], ...)
 4: lapply(X = X, FUN = FUN, ...)
 3: sapply(1:n.nodes, function(i) {
        kns =
        if (node.types[1] == "gene")

            items =
        else items = kns
        ord = order(items)
        items = items[ord]
        kns = kns[ord]
        hit = items %in% genes
        if (sum(hit) == 0) {
    return(c(kns[1], spacials[i, ], rep(NA,
        else if (sum(hit) == 1) {
            edata =
 mol.data[as.character(items[hit]), ]
    return(c(kns[hit], spacials[i, ], edata))
        else {
            node.sum =
            edata =
    ]), 2, node.sum, na.rm = T)
    return(c(kns[hit][1], spacials[i, ],
 2: node.map(gene.data, node.data, node.types =
 gene.node.type, node.sum = node.sum)
 1: pathview(gene.data = data_bac_values, pathway.id =
 "05132", species = "sey", 
        out.suffix = "test",
 kegg.native = T, same.layer = F)

 I'm aware from the mailing list that KEGG is not very
 consistant with their ID scheme, which causes trouble. I
 rechecked, the Id I use (Refseq locus tag) is also used by
 KEGG (e.g. http://www.genome.jp/dbget-bin/www_bget?sey:SL1344_0001
 works fine); I tried it with other IDs which I specified via
 gene.idtype and get the error:

 > pv.out <- pathview(gene.data = data_bac_values,
 gene.idtype = "UNIPROT", pathway.id = "05132" ,species =
 "sey", out.suffix = "test", kegg.native = T, same.layer =
 Error in pathview(gene.data = data_bac_values, gene.idtype =
 "UNIPROT",  : 
[[elided Yahoo spam]]

 This is also truefor other IDs (of course I change each time
 the input file accordingly).

 Do you have any idea what causes the problem? any hint would
 be very much appreciated. Thank you very much in advance.


  -- output of sessionInfo(): 

 > sessionInfo()
 R version 3.0.1 (2013-05-16)
 Platform: x86_64-redhat-linux-gnu (64-bit)

  [1] LC_CTYPE=en_US.UTF-8   
  [3] LC_TIME=en_US.UTF-8       
  [5] LC_MONETARY=en_US.UTF-8   
  [7] LC_PAPER=C           
  [9] LC_ADDRESS=C           

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

 other attached packages:
  [1] pathview_1.1.4   
    org.Hs.eg.db_2.9.0   RSQLite_0.11.4 
  [4] DBI_0.2-7           
 AnnotationDbi_1.22.6 Biobase_2.20.1      
 BiocGenerics_0.6.0   KEGGgraph_1.16.0 
 [10] XML_3.98-1.1        

 loaded via a namespace (and not attached):
 [1] grid_3.0.1      IRanges_1.18.4 
 png_0.1-6       Rgraphviz_2.4.1
 [5] stats4_3.0.1    tools_3.0.1    

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