Hi,

This may be super basic, but I'm really stuck. I am running enricher (the generic version because I'm not using a model-organism) and I am supplying my own list of GO terms.

I run it like this:

ego_bp_aga <- enricher(gene = aga_genes,
                       TERM2GENE = go_terms)

I then want to create a dotplot

dotplot(ego_bp_aga, showCategory=30)

I get a dotplot that looks good, except that on the y-axis it shows GO IDs instead of terms. Is this because I have to add TERM2NAME when I first run enricher? If this is the case, how do I get the GO terms from my list of GO IDs?

Yes, TERM2NAME is needed to map the GOID to its term (description).

An easy way of obtaining this mapping is by extracting the information from the Bioconductor GO annotation database package (GO.db).

> library(GO.db)
> # extract a named vector of all terms
> goterms <- Term(GOTERM)
> 
> #convert into a data frame
> term2name <- data.frame("GOID"=names(goterms),"term"=goterms )
> 
> head(term2name)
                 GOID                                                     term
GO:0000001 GO:0000001                                mitochondrion inheritance
GO:0000002 GO:0000002                         mitochondrial genome maintenance
GO:0000003 GO:0000003                                             reproduction
GO:0000006 GO:0000006    high-affinity zinc transmembrane transporter activity
GO:0000007 GO:0000007 low-affinity zinc ion transmembrane transporter activity
GO:0000009 GO:0000009                   alpha-1,6-mannosyltransferase activity
>

term2name can then be used when calling the function enrichr, by specifying TERM2NAME=term2name.

Be sure, though, to check that term2name contains all GOIDs present in your TERM2GENE mapping (thus your object go_terms).