is it possible to obtain a NES score for each cell and overlay it on umap? #4710
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Not sure what the NES score is but if you have any numeric data per cell you can overlay it on the UMAP representation. If you add the data as metadata in the Seurat object, you can then specify that value using the |
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Hi Tim,
Thank you so much for your reply.
My question, may need to reword it, is sort of divided into two: 1. can I do GSEA in each cell (normally is performed between two conditions or within a sample ssGSEA) to identify enriched pathways (hallmarks) for each cell. As output from the analysis (2) , hypothetically we could get Normalised enriched scores (NES) for each pathway/hallmark and each cell and based on your reply be able to overlay it on umap using the Feature plot() function, which is great. However, unsure I am unsure if there is a tool to perform single cell GSEA. Any feedback/ideas will be greatly appreciated.
Cheers,
Carlos
Carlos Aya-Bonilla BSc., MSc., PhD
Jerome Lejeune Foundation Post-Doctoral Research Fellow | Leukaemia and Cancer Genetics |Telethon Kids Institute
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From: Tim Stuart ***@***.***>
Reply to: satijalab/seurat ***@***.***>
Date: Saturday, 3 July 2021 at 12:46 am
To: satijalab/seurat ***@***.***>
Cc: Carlos Aya-Bonilla ***@***.***>, Author ***@***.***>
Subject: Re: [satijalab/seurat] is it possible to obtain a NES score for each cell and overlay it on umap? (#4710)
Not sure what the NES score is but if you have any numeric data per cell you can overlay it on the UMAP representation. If you add the data as metadata in the Seurat object, you can then specify that value using the features parameter in FeaturePlot(). See the documentation for FeaturePlot() for more
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Maybe what you're looking for is more of a module score: https://www.rdocumentation.org/packages/Seurat/versions/4.0.3/topics/AddModuleScore |
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@carlosaya2 Cheers, |
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Hi, it is my understanding that GSEA NES is obtained by interrogating the DEGs of each cluster in MSigDB hallmarks, is it possible to obtain the NES of each hallmark per cell and overlay it on umap plots? I will highly appreciate your feedback. cheers
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