How to create an upset plot with a count of genes per pathway in cluster-profiler?
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7 days ago
DN99 • 0

I'm plotting an upset plot of KEGG enriched pathways using DOSE and clusterprofiler which works fine like this:

kk <- enrichKEGG(gene = gene_ids,
                 organism     = 'hsa',
                 pvalueCutoff = 0.05,
                 pAdjustMethod = 'fdr')

upsetplot(kk)

The plot given looks like this: upset plot

I'm wondering if there's a way to expand this plot on the left to have a bar chart of the number of genes enriched per pathway? So the style of the plot would expand to look like this:

upset2

Is this possible using the upsetplot() function? Or would I need to try plotting the kk data with another package like UpSetR?

enrichment R dose plot gene upset • 59 views
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