Question

gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets

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Cen • 0

@5b5268ee

Last seen 6 months ago

United States

clusterProfiler implemented GSEA plot that mimic broad Institute's GSEA software in gseaplot2. Does anyone knows how to use gseaplot2 to compare two datasets? In GSEA you can do this by providing a gene set that contains the top genes from the first dataset and use GSEA to analyze that gene set against the second gene set.

Thank you in advance for your help!

enrichplot GSEA clusterProfiler • 1.3k views

ADD COMMENT • link updated 6 months ago by Fatemeh • 0 • written 9 months ago by Cen • 0

score 0 · Answer 1 · 2023-08-10

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 2 days ago

United States

The default for clusterProfiler is to use fgsea from the eponymous package. Which would be simple to use directly (see ?fgsea).

ADD COMMENT • link 9 months ago James W. MacDonald 65k

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Thanks for your comment. I was able to use fgsea for comparing two datasets but I liked the plot generated by gseaplot2.

I tried to input the object returned by fgsea to gseaplot2 but it doesn't like it.

This is the command to generate plot enrichment in fgsea which in this case, I can change the 175th entry in examplePathways to my second dataset.

data(examplePathways)
data(exampleRanks)
fgseaRes1 <- fgsea(examplePathways[[175]], exampleRanks)
plotEnrichment(examplePathways[[175]],exampleRanks)

But, the question is how to do similar thing and get plot enrichment using gseaplot2 ?