clusterprofiler dotplot facet_grid plot based on ONTOLOGY

Question

[Omics data mining]

Hello everyone

I am using clusterProfiler for gene enrichment analysis against GO terms (MF, BP and CC). For dotplot, I used facet_grid based on the "ONTOLOGY" in the data frame. I am interested in generating same type of plot as shown here https://freeimage.host/i/go-dot-3dv5d.2nDmuV

k1_all <- enrichGO(unique(ids$ENTREZID), OrgDb = org.Hs.eg.db, ont = "ALL", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05, readable = TRUE)

dotplot(k1_all, showCategory = 20) + facet_grid(ONTOLOGY ~.)

But I am getting only BP category in output file.

Please let me know if I am doing something wrong. I would appreciate all the suggestions.

[Basti]

This is probably because your 20 first categories are only BP (argument showCategory is set to 20). You may create a sub-dataset with the top categories for each ontology.

[Omics data mining]

It worked after subset. Thanks alot.