[BioC] pathview -- ID Problem?

[Luo Weijun]

Dear Fabian,
You need to update your pathview to the latest release version, which is 1.2.0. It is at:
http://bioconductor.org/packages/release/bioc/html/pathview.html
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.
Weijun

--------------------------------------------


 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
 run.

 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

 head(data_bac_values)
 SL1344_0001 SL1344_0002 SL1344_0003 SL1344_0004 SL1344_0005
 SL1344_0006 
   0.1329739   0.4947647 
 -1.4013626   0.5086116  -4.0000000 
 -0.2028169 

 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
 this:

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

            items =
 as.numeric(kns)
        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,
 ncol(mol.data))))
        }
        else if (sum(hit) == 1) {
            edata =
 mol.data[as.character(items[hit]), ]
        
    return(c(kns[hit], spacials[i, ], edata))
        }
        else {
            node.sum =
 eval(as.name(node.sum))
            edata =
 apply(cbind(mol.data[as.character(items[hit]), 
            
    ]), 2, node.sum, na.rm = T)
        
    return(c(kns[hit][1], spacials[i, ],
 edata))
        }
    })
 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 =
 F)
 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.

 best
 Fabian

  -- output of sessionInfo(): 

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

 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=C           
      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  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      
  [7]
 BiocGenerics_0.6.0   KEGGgraph_1.16.0 
    graph_1.38.3        
 [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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