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

Question

[Amr]

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?

Answer 1

[Basti]

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

[Amr]

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"’

[Basti]

Follow carefully the tutorial, you should not convert the GSEA result into a dataframe and select any result from the GSEA result : https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html