Hi,

I'm a bio informatics student, who is just starting with R and pathview. I normalised an expression dataset, to the point where i only have to columns (one is the gene_id, and one the fold change).

My file looks like this:

I've tried to read this into R, with this code.

> dataFC<-read.csv("D:/Users/Dani/Documents/School/OWE6B/readTopathview.csv",header = T, sep =";")
> head(dataFC)
> keggcode <- "sce"
> data(gene.idtype.list)
> gene.idtype.list
> library(KEGGREST)
> pathways <- keggList("pathway", keggcode)
> head(pathways)

> pv.out <- pathview(gene.data = dataFC, gene.idtype = "KEGG", 
                   pathway.id = "00620", species = keggcode, out.suffix = "00620", keys.align = "y", kegg.native = TRUE, key.pos = "topright")

The result however is that no genes are mapped. i get this message

Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory D:/Users/Dani/Documents
Info: Writing image file sce00620.00620.png
Warning message:
In colnames(plot.data)[c(1, 3, 9:ncs)] = c("kegg.names", "all.mapped",  :
  number of items to replace is not a multiple of replacement length

How do I fix this, What am I doing wrong ( i have read the corresponsing pathview guide, but i just can't figure out why it's not working)

thanks in advance,

Dani

Well I solved it myself. Maybe i can help someone with it. Pathview only accepts genes as row names so not as a column. I didn't find it in the guide so maybe this is worth adding?

Sadly i had a file with duplicate genes so what i decided to do was the following:

dataFC<-read.csv("D:/Users/Dani/Documents/School/OWE6B/readTopathview.csv",header = T, sep =";")
head(dataFC)
keggcode <- "sce"
library(pathview)
library(KEGGREST)
datagene <- subset(dataFC, select = "ORF")
dataFold <- subset(dataFC, select = "FC")
df <- data.frame(matrix(ncol = 2, nrow = 6153))
datageneORF <-unlist(datagene)
dataFoldun = unlist(dataFold)
df[1] = datagene
df[2] = dataFoldun
rownames(df) = make.names(df[,1], unique=TRUE)
df[,1] <- NULL

pv.out <- pathview(gene.data = df, gene.idtype = "KEGG", 
                   pathway.id = "sce00010", species = keggcode, out.suffix = "Glycolysis", keys.align = "y", 
                   kegg.native = TRUE, key.pos = "topright")
pv.out <- pathview