summarize_counts
- scib.preprocessing.summarize_counts(adata, count_matrix=None, mt_gene_regex='^MT-')
Summarise counts of the given count matrix
This function is useful for quality control. Aggregates counts per cell and per gene as well as mitochondrial fraction.
- Parameters
count_matrix – count matrix, by default uses
adata.Xmt_gene_regex – regex string for identifying mitochondrial genes
- Returns
Include the following keys in
adata.obs‘n_counts’: number of counts per cell (count depth) ‘log_counts’:np.logof counts per cell ‘n_genes’: number of counts per gene ‘mito_frac’: percent of mitochondrial gene counts as an indicator of cell viability