clusterprofiler dotplot and cnetplot showCategory isn't working

Question

[pajnra]

Hi,

I ran a KEGG overrep analysis using clusterprofiler and tried to plot them via dotplot and cnetplot but only the top two categories are showing. I've tried using showCategory and tried selecting the pathways.

I've tried

selected_pathways <- (Adult_KEGG$Description[1:10])

and this was the output:

selected_pathways 2 "Pyruvate metabolism" "Glucagon signaling pathway" [3] NA NA
[5] NA NA
[7] NA NA
[9] NA NA

Below is my code and output:

Adult_KEGG <- enrichKEGG(gene = Adultsig, organism = "rno",
                         pvalueCutoff = 2)
Adult_KEGG <- setReadable(Adult_KEGG, OrgDb = org.Rn.eg.db, keyType="ENTREZID")

Adultcp <- cnetplot(Adult_KEGG, shadowtext = 'none', showCategory = 5,
                    foldChange = fold_changesAdult)`

Answer 1

[pajnra]

I figure it out by adjusting my qvalueCutoff.