snapatac2.pl.coverage#

snapatac2.pl.coverage(adata, region, groupby, out_file=None)[source]#

Plot the coverage tracks for different groups of cells. This function requires matplotlib to be installed.

This is a simple implementation for quick visualization. For more advanced visualization, please consider exporting the data using export_coverage and visualize it using a genome browser.

Parameters:

adata (AnnData) – Annotated data matrix.
region (str) – Genomic region, e.g. ‘chr1:100000-200000’.
groupby (str | list[str]) – Group the cells into different groups. If a str, groups are obtained from .obs[groupby].
out_file (str | None) – Path of the output file for saving the output image.