[BioC] Doubts regarding Pathview

[Luo Weijun]

your input data need to be a matrix or a vector named with compound IDs. you will need to do:
cnames=met[,1]
met=met[,2]
names(met)=cnames
head(met)

then call pathview function. you may need to specify both.dir=F and adjust limit values, given your data are not fold changes. Please alway read function documents:
?pathview
and package tutorial:
http://www.bioconductor.org/packages/release/bioc/html/pathview.html


--------------------------------------------
On Sat, 8/2/14, sanchari sircar wrote:

 Subject: Fwd: Doubts regarding Pathview

 Date: Saturday, August 2, 2014, 2:43 PM

 Dear Sir,

 In continuation to the
 previous mail, I have attached a small input filet, this is
 what I am doing:

 library(pathview)

 > met=read.table("met3.txt",
 sep='\t')
 > met
       V1   V2
 1
 C05433 10.0
 2 C02094 33.9
 3
 C08586 10.0
 4 C05430 10.0
 5
 C05432 10.0
 6 C05413 10.0
 7
 C08614  0.4

 > pv.out
 <- pathview(cpd.data = met, pathway.id =
 "00906",
 + species =
 "sly", out.suffix = "sly_v1",
 kegg.native = T)

 No
 annotation package for the species sly, gene symbols not
 mapped!
 No of the genes or compounds mapped
 to the pathway!
 Argument gene.idtype or
 cpd.idtype may be wrong.
 Working in
 directory D:/path_view
 Writing image file
 sly00906.sly_v1.png
 Warning message:
 In colnames(plot.data)[c(1, 8:ncs)] =
 c("kegg.names", colnames(mol.data)) :
   number of items to replace is not a multiple
 of replacement length

 >
 str(pv.out)
 List of 2
  $
 plot.data.gene:'data.frame': 48 obs. of  9
 variables:
   ..$ kegg.names: chr [1:48]
 "544104" "544104" "543649"
 "544129" ...
   ..$ labels    :
 chr [1:48] "101267662" "101267662"
 "543649" "CrtL-e-1" ...
   ..$ type      : chr [1:48]
 "gene" "gene" "gene"
 "gene" ...
   ..$ x     
    : num [1:48] 351 351 1369 890 1182 ...
   ..$ y         : num [1:48] 706
 569 770 284 365 367 678 952 828 828 ...
  
 ..$ width     : num [1:48] 46 46 46 46 46 46 46
 46 46 46 ...
   ..$ height    : num [1:48]
 17 17 17 17 17 17 17 17 17 17 ...
   ..$
 kegg.names: num [1:48] 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': 114
 obs. of  9 variables:
   ..$ kegg.names:
 chr [1:114] "C16486" "C16340"
 "C16291" "C05434" ...
  
 ..$ labels    : chr [1:114] "C16486"
 "C16340" "C16291" "C05434"
 ...
   ..$ type      : chr [1:114]
 "compound" "compound"
 "compound" "compound" ...
   ..$ x         : num [1:114]
 1108 939 351 351 1172 ...
   ..$ y     
    : num [1:114] 951 596 767 657 540 590 365 282
 229 155 ...
   ..$ width     :
 num [1:114] 8 8 8 8 8 8 8 8 8 8 ...
   ..$
 height    : num [1:114] 8 8 8 8 8 8 8 8 8 8 ...
   ..$ V1        : num [1:114] 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 ...

 >
 head(pv.out$plot.data.cpd)
     kegg.names
 labels     type    x   y width
 height V1 mol.col
 84      C16486 C16486
 compound 1108 951     8      8 NA #FFFFFF
 86      C16340 C16340 compound  939 596 
    8      8 NA #FFFFFF
 87   
   C16291 C16291 compound  351 767     8   
   8 NA #FFFFFF
 88      C05434 C05434
 compound  351 657     8      8 NA #FFFFFF
 102     C16284 C16284 compound 1172
 540     8      8 NA #FFFFFF
 103     C16282 C16282 compound 1172
 590     8      8 NA #FFFFFF


 The kegg
 graphs are getting downloaded, but they are not colored. 

 Kindly Help.

 Thanking You,
 Sanchari