Question: pathview R package not working
2
gravatar for catechize.2.learn
21 months ago by
catechize.2.learn120 wrote:

Hi!

I cannot make any useful plots in pathviews. Where am I going wrong?

library(pathview)
a= c( -2,4)
names(a) =c('MDM2', 'TP53')
pathview(gene.data = a, pathway.id = "04115", species = "hsa")

there is no highlighting of either p53 or mdm2 in the resulting fig.

pathview R • 924 views
ADD COMMENTlink modified 13 months ago by murshad.60ali10 • written 21 months ago by catechize.2.learn120
1

I think the answers is on the warnings you get:

Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
ADD REPLYlink written 21 months ago by LluĂ­s R.910
6
gravatar for Benn
21 months ago by
Benn8.0k
Netherlands
Benn8.0k wrote:

You can't use the gene names (symbols), but have to use ENTREZ gene IDs.

library(pathview)
a= c( -2,4)
names(a) =c("4193", "7157")
pathview(gene.data = a, pathway.id = "04115", species = "hsa")

To get these entrez IDs you can use org.Hs.eg.db in R.

library(org.Hs.eg.db)
symbols = c("MDM2","TP53") 
names(a) <- mget(symbols, revmap(org.Hs.egSYMBOL),ifnotfound=NA)
ADD COMMENTlink modified 21 months ago • written 21 months ago by Benn8.0k
1

Thank you indeed very much @b.nota

ADD REPLYlink written 21 months ago by catechize.2.learn120
0
gravatar for murshad.60ali
13 months ago by
murshad.60ali10 wrote:

Thank you.....FOR KEGG RESULTS HIGHLIGHTED THE TARGETED GENES

ADD COMMENTlink written 13 months ago by murshad.60ali10
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