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.obs['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?