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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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DEenrichRPlot positive and negative results are the same #7500

Closed abspangler13 closed 1 month ago

abspangler13 commented 1 year ago

Hello,

I'm running Seurat 4.2.0 and using the DEenrichRPlot() function. I'd like to see the enriched pathways for both negative and positive DE genes. For some reason, the function returns the exact same pathways and and p-values for both the negative and positive DE genes for all of my clusters. I'm running the function like this:

lapply(clusters, FUN = function(x) { DEenrichRPlot(tonsil_in, ident.1 = x,logfc.threshold = 0.4,enrich.database = "GO_Biological_Process_2023",max.genes = 200, balanced = FALSE) })

And my plots look like this:

image image

Thanks for your help,

Abby

longmanz commented 1 year ago

Hi, This is indeed a bug. Sorry. We will be fixing this soon. See https://github.com/satijalab/seurat/issues/7492.

dcollins15 commented 1 month ago

Thanks for using Seurat!

It appears that this issue has gone stale. In an effort to keep our Issues board from getting more unruly than it already is, we’re going to begin closing out issues that haven’t had any activity since the release of v4.4.0.

If this issue is still relevant we strongly encourage you to reopen or repost it, especially if you didn’t initially receive a response from us.