I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.

I did the below:

bulk_de_genes_up_list = bulk_de_genes['Gene'].tolist()
#Subset the data based on the list of genes
adata2 = adata[:, adata.var_names.isin(bulk_de_genes_up_list)]
average_expression = adata2.X.mean(axis=1)
adata2.var['bulk_de_gene_average'] = average_expression
sc.pl.umap(adata2, color='bulk_de_gene_average', cmap='viridis')

I do get a UMAP as an output but I am not sure if it is done correctly. I am mainly worried about average_expression = adata2.X.mean(axis=1)

Is that the correct way of calculating the mean of the gene expression per cell?

Thank you



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