Entering edit mode
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!
Thanks for your comment. I was able to use
fgsea
for comparing two datasets but I liked the plot generated bygseaplot2
.I tried to input the object returned by
fgsea
togseaplot2
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.But, the question is how to do similar thing and get plot enrichment using
gseaplot2
?Hi Jemes, did you find a way to do so, I am struggling with the same issue