ClusterProfiler dotplot method does not include all input groups.
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16 months ago
markm014 ▴ 10

I am using the clusterProfiler methods enrichGO and dotplot to do some downstream differential expression analysis. I invoke enrichGO with the following call:

formula_res = compareCluster(`EntrezGene ID~Direction+Treatment, data=filtered_data, fun="enrichGO", OrgDb="org.Hs.eg.db", ont="BP", qvalueCutoff= 0.2, readable=TRUE)

where filtered_data is a dataframe with the follwoing columns:

Gene, EntrezGene ID, Gene Stable ID, Name, Treatment, Direction

Then, plot via the call to dotplot:

p = dotplot(formula_res, showCategory=10, title="test", font.size=9, includeAll = TRUE)

I am surprised that if I have in my data frame 8 unique combinations of treatment and direction (Ex: four different treatments with both up and down regulated genes for each) my dotplot often outputs less groups. For instance, I often get a plot with six groups shown despite having eight "input groups" (as defined by unique combination of direction + treatment).

I have read the documentation and tried setting showCategory to NULL instead of 10, which the documentation says should force a return of all groups, but still not all treatments are included. Am I missing something obvious on this one? I want to verify my results are not erroneous.

clusterProfiler R dotplot differential expression • 589 views
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If it doesn't find any enriched terms for a group that group probably doesn't get added to the result. Try running enrichGO on some of the groups that didn't appear in your results.

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Thank you for taking the time to answer. The thing is, when I run the enrichGo function on each of the 8 input groups separately with the same parameters, they all 8 have significant GO terms. Sorry, I should have included this above!

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