stereo.core.StPipeline.cal_qc#
- StPipeline.cal_qc()[source]#
Calculate the key indicators of quality control.
- Observation level metrics include:
total_counts: total number of counts for a cell.
n_genes_by_count: number of genes expressed of counts for a cell.
pct_counts_mt: percentage of total counts in a cell which are mitochondrial.
- Return type:
A StereoExpData object storing quality control indicators, including two levels of obs (cell) and var (gene).