markers to define a cell population in a single UMAP
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18 months ago
Morris_Chair ▴ 240

Hello guys,

I'm doing single cells analysis using Seurat pipeline and after the cluster distribution (UMAP) I found markers unregulated and downregulated in each of them. I want to know if it's possible to define in a single UMAP plot a specific cluster by including or excluding specific markers for example:

Cluster 1: A+B+C- Cluster 2 A+B-C+ Cluster 3 A-B+C+

Does exist a code that when I give the information (A+B-C+) automatically defines and shows in UMAP the cluster 2?

Or is it possible represent all of three markers in only one plot?

Thanks for help

RNA-Seq scRNA-seq Seurat • 680 views
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Can you explain a bit more? Do you want to make a new clustering with all cells (or only some cells?) based on these genes? Or do you want to color cells by gene expression? I do not really understand.

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Hi ATpoint,

I want to make a new clustering with all cells based on three selected genes.

Thank you

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It is possible to use custom dimensional reductions in Seurat, please check https://satijalab.org/seurat/v3.0/dim_reduction_vignette.html

Storing a custom dimensional reduction calculation is the passage you probably want. This then would include only the genes you want. Not discussing if a clustering based on three genes actually makes sense (in fact I do not know).

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ok sorry I was not clear, I don't have to make a UMAP only using three genes but I want to show where the cells that express this genes are located. For example if I have three population of cells in the UMAP and the population 2 is A+ B- C+, I want to show cells A+ and C+ instead of two separated UMAP with a single marker A and C