fGSEA collapsePathways function not working

fGSEA collapsePathways function not working

0

Hello all,

I’m running the package fgsea and I’m having trouble with the collapsePathways function. When not using that function, I get the expected data frame with 8 columns (pathway, pval, NES, etc.) that I can then plot using ggplot. However, when I try to use collapsePathways, the output is a data frame with just the collapsed pathway names, meaning I have nothing to actually plot. Anybody know what’s wrong with the script below?

fgseaRes <- fgsea(pathways=pathways.hallmark, 
                  minSize  = 15,
                  maxSize  = 1000,
                  eps = 0.0,
                  stats=ranks)
fgseaRes

fgseaRes <- collapsePathways(
              fgseaRes,
              pathways=pathways.hallmark,
              stats=ranks,
              pval.threshold = 0.05)

fgseaResTidy <- fgseaRes %>%   as_tibble() %>%   arrange(desc(NES))

fgseaResTidy <- apply(fgseaResTidy,2,as.character)

g <- ggplot(fgseaResTidy, aes(reorder(pathway, NES), NES))

g + geom_col(aes(fill=padj<0.05)) + coord_flip() + labs(x="Pathway", y="Normalized Enrichment Score", title="Hallmark Pathways NES from GSEA") + theme(axis.text.y = element_text(size = 2)) + theme_minimal()


fgsea

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