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