Entering edit mode
2.3 years ago
pajnra
▴
10
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)`