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Co-expression of markers in single cells using scanpy

Hello,

I am new to the world of single cell analysis, but scanpy has been useful for my analyses so far. However, I want some way to visualise the co-expression of two marker genes in single cells on a UMAP. I noticed that Seurat has a nice way to show this using Feature Plot and blend:

enter image description here

I am not familiar with R. Does anybody know if there an easy way to do this using scanpy/pytjon based methods?

scanpy co-expression single-cell
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written by A.rex2 • A.rex2

You could do something like this- It will be very close to seurat.

gene_list = ['MS4A1', 'CD79A']
sc.tl.score_genes(adata, gene_list, score_name='MS4A1_CD79A')
sc.pl.umap(adata, color='MS4A1_CD79A')

enter image description here

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written by bk11 • bk11

Thank you. However, I think this does not account for the case of intermediate expression of two markers in a single cell. E.g one cell had high expression of only GeneA, another cell has high expression of Gene B, and a third intermediate expression of A+B, the UMAP will look uniform. Have I got that right?

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written by A.rex2 • A.rex2

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