Enrichment plot function in STUtility

[krigia]

Hello @jbergenstrahle @ludvigla @davidecrs

Does STutility have any option/function to generate enrichment spatial plots and UMAPs for Visium data? Similar to those generated by another pipeline for spatial analysis:

Thank you.

[ludvigla]

Hi @krigia,

Could you please elaborate a little? If the goal is simply to calculate an enrichment score based on a gene set there are some options available. You could for example use the AddModuleScore function from Seurat to compute an enrichment score that can be plotted with FeaturePlot on a UMAP or with ST.FeaturePlot to visualize it spatially.

Another option is to use the fgsea R package to compute enrichment scores. AUcell and Ucell might also be interesting alternatives.

Cheers, Ludvig

[krigia]

@ludvigla Thank you. I was able to run AddModuleScore and estimate an enrichment score for each spot. Is there any way to estimate an enrichment score for each cluster separately (and no individual spot)? Thank you!