Hi Biostar,

I try to make plot as the fgsea tutorial using the same code:

stats <- with(results, setNames(logFC, row.names(results)))
fgseaRes <- fgsea(pathways = c2_list, stats = stats, minSize=15, maxSize=500)
topPathwaysUp <- fgseaRes[ES > 0][head(order(pval), n=10), pathway]
topPathwaysDown <- fgseaRes[ES < 0][head(order(pval), n=10), pathway]
topPathways <- c(topPathwaysUp, rev(topPathwaysDown))
plotGseaTable(topPathways, stats, fgseaRes, 
              gseaParam=0.5)

https://bioconductor.org/packages/devel/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html Would you please have a suggestion? topPathwaysUp, topPathwaysDown and topPathways have the correct values. Can't attach the figure to illustrate the issue here (image:Exceeded the maximum amount of images you can upload). Thank you so much!

Update: this worked.

plotGseaTable(c2_list[topPathways], stats, fgseaRes, 
              gseaParam=1)