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What is the best way to visualize the enrichment plots together after obtaining them from GSEA report?

What is the best way to visualize the enrichment plots together after obtaining them from GSEA report? Is there a way to plot the enrichment scores (ES) for different gene sets together?

es enrichment_plot gsea
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updated by Basti • Basti • written by Amr • Amr

1 answer

You could draw a gseaplot : https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html?q=gseaplot#running-score-and-preranked-list-of-gsea-result

Otherwise clusterProfiler package offers many alternatives

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written by Basti • Basti

I did that code:

ddd <- as.data.frame(ddd$ES) #ES is the enrichment score and ddd is the file which has ES, NES, NOM-pvalue etc

p1<- gseaplot(ddd, geneSetID = 1, by = "runningScore", title = ddd$NAME[1]) #NAME is the name of gene sets

p2 <- gseaplot(ddd, geneSetID = 1, by = "preranked", title = ddd$NAME[1])

p3 <- gseaplot(ddd, geneSetID = 1, title = ddd$NAME[1])

cowplot::plot_grid(p1, p2, p3, ncol=1, labels=LETTERS[1:3])

and I got that error Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘gseaplot’ for signature ‘"data.frame"’

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written by Amr • Amr

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