[BioC] pathview -- ID Problem?

[Luo Weijun]

There was a typo in my original response, id.type should be gene.idtype. The correct one is:
..., for you data, you need to specify gene.idtype="kegg" with pathview. 
pv.out <- pathview(gene.data = data_bac_values, pathway.id = "05132", species = "sey", gene.idtype ="kegg", out.suffix = "test", kegg.native = T, same.layer = F)
Weijun

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


 Subject: Re: pathview -- ID Problem?

 Date: Friday, October 18, 2013, 2:53 PM

 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

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


 wrote:

  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    
  
  
  --
  Sent via the guest posting facility at bioconductor.org.