[BioC] Pathview: all NA's in the mapped gene data

[Luo Weijun]

Vishal,
In your example, you have to specify gene.idtype="SYMBOL" (either upper or lower case is fine here) when calling pathview function. 
pv.ting <- pathview(gene.data = geneV[,1], pathway.id = "05200",species = "mmu", gene.idtype="SYMBOL", out.suffix = "test2", kegg.native = T,same.layer = F)
The default gene.idtype="entrez", and pathview take your input as Entrez Gene ID hence can’t map any of your gene data onto the specified pathway. Therefore, you get #FFFFFF (white) nodes, which corresponds to NA values or “no mapped data”. If you haven’t, pathview will install the "org.Mm.eg.db" package, which is needed for mapping the gene symbol to entrez gene id. Make sure you use the official gene symbols for your data. Let me know how that goes.
For details check the help page for pathview function and look under argument “gene.idtype”. HTH.
Weijun


On 7/11/2013 1:59 PM, Thapar, Vishal wrote:
> Hi Weijun,
> 
> In terms of Pathview, i am having some issues. I hope you can help me here..
> 
> Basically, I am trying to give path view a vector with expression values and the names of the vector has the gene names. I believe that is what the function needs but its not giving me the right out put. Let me show u how:
> 
> So this is the vector that we give in the vignette:
>   head(gse16873.d[, 1])
>        10000       10001       10002       10003   100048912       10004
> -0.30764480  0.41586805  0.19854925 -0.23155297 -0.04490724 -0.08756237
> 
> This is my vector:
>   head(geneV[,1])
>     Upk3b     Ier2     Egr1   Nkain4   Igfbp5   Slc6a4
> 2.572087 2.075237 2.725171 1.674379 3.265937 1.839275
> 
> This is the my command:
> pv.ting <- pathview(gene.data = geneV[,1], pathway.id = "05200",species = "mmu", out.suffix = "test2", kegg.native = T,same.layer = F)
>   
> Problem is that when we do
> head(pv.out$plot.data.gene)
>    kegg.names labels type   x   y width height   mol.data mol.col
> 1       1029 CDKN2A gene 532 124    46     17  0.1291987 #BEBEBE
> 2      51343   FZR1 gene 919 536    46     17 -0.4043256 #5FDF5F
> 3       4171   MCM2 gene 553 556    46     17 -0.4202181 #5FDF5F
> 4       4998   ORC1 gene 494 556    46     17  0.9864873 #FF0000
> 5        996  CDC27 gene 919 297    46     17  1.1811525 #FF0000
> 6        996  CDC27 gene 919 519    46     17  1.1811525 #FF0000
> 
> 
> when i do that for my output
> head(pv.ting$plot.data.gene)
>    kegg.names labels type   x   y width height mol.data mol.col
> 2      13176    Dcc gene 133 221    46     17       NA #FFFFFF
> 3      12367  Casp3 gene 215 189    46     17       NA #FFFFFF
> 4      12371  Casp9 gene 279 211    46     17       NA #FFFFFF
> 5      12367  Casp3 gene 415 221    46     17       NA #FFFFFF
> 6      12550   Cdh1 gene 133 348    46     17       NA #FFFFFF
> 7      12387 Ctnnb1 gene 179 348    46     17       NA #FFFFFF
> 
> str(pv.ting)
> List of 2
>   $ plot.data.gene:'data.frame':	201 obs. of  9 variables:
>    ..$ kegg.names: chr [1:201] "13176" "12367" "12371" "12367" ...
>    ..$ labels    : chr [1:201] "Dcc" "Casp3" "Casp9" "Casp3" ...
>    ..$ type      : chr [1:201] "gene" "gene" "gene" "gene" ...
>    ..$ x         : num [1:201] 133 215 279 415 133 179 54 193 391 133 ...
>    ..$ y         : num [1:201] 221 189 211 221 348 348 419 331 349 554 ...
>    ..$ width     : num [1:201] 46 46 46 46 46 46 46 46 46 46 ...
>    ..$ height    : num [1:201] 17 17 17 17 17 17 17 17 17 17 ...
>    ..$ mol.data  : num [1:201] NA NA NA NA NA NA NA NA NA NA ...
>    ..$ mol.col   : Factor w/ 1 level "#FFFFFF": 1 1 1 1 1 1 1 1 1 1 ...
>   $ plot.data.cpd :'data.frame':	13 obs. of  9 variables:
>    ..$ kegg.names: chr [1:13] "C00280" "C00187" "C05981" "C00165" ...
>    ..$ labels    : chr [1:13] "C00951" "C00187" "C05981" "C00165" ...
>    ..$ type      : chr [1:13] "compound" "compound" "compound" "compound" ...
>    ..$ x         : num [1:13] 642 798 452 284 284 ...
>    ..$ y         : num [1:13] 30 32 660 1164 1202 ...
>    ..$ width     : num [1:13] 8 8 8 8 8 8 8 8 8 8 ...
>    ..$ height    : num [1:13] 8 8 8 8 8 8 8 8 8 8 ...
>    ..$ kegg.names: num [1:13] NA NA NA NA NA NA NA NA NA NA ...
>    ..$ mol.col   : Factor w/ 1 level "#FFFFFF": 1 1 1 1 1 1 1 1 1 1 …
> 
> So clearly there is something going one where by its not getting NA if mol.data… and the mol.col is always FFFF
> 
> Any idea what i am doing wrong here?
> 
> Thanks,
> 
> Vishal