Initial gene filtering¶
Show and apply gene filtering¶
-
cell2location.utils.filtering.
filter_genes
(adata, cell_count_cutoff=15, cell_percentage_cutoff2=0.05, nonz_mean_cutoff=1.12)[source]¶ Plot the gene filter given a set of cutoffs and return resulting list of genes.
- Parameters
adata – anndata object with single cell / nucleus data.
cell_count_cutoff – All genes detected in less than cell_count_cutoff cells will be excluded.
cell_percentage_cutoff2 – All genes detected in at least this percentage of cells will be included.
nonz_mean_cutoff – genes detected in the number of cells between the above mentioned cutoffs are selected only when their average expression in non-zero cells is above this cutoff.
- Returns
- Return type
a list of selected var_names