snapatac2.pl.coverage#

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

Plot coverage tracks for grouped cells across one genomic region.

Use this function for quick local inspection of coverage patterns. Install matplotlib before calling it.

This is a simple implementation for quick visualization. For more advanced visualization, export the data with snapatac2.ex.export_coverage and inspect it in a genome browser.

Anti-Patterns#

  • Do NOT use this function for publication-scale genome browser tracks; export coverage files instead.

  • Do NOT pass multiple genomic intervals. region must be a single string formatted as "chrom:start-end".

param adata:

Annotated data matrix with fragments available for coverage retrieval.

type adata:

AnnData

param region:

Genomic interval to plot, formatted as "chrom:start-end"; for example, "chr1:100000-200000".

type region:

str

param groupby:

Cell grouping definition. If a string, groups are read from adata.obs[groupby].

type groupby:

str | list[str]

param out_file:

Output path for saving the Matplotlib figure. If None, display the plot with matplotlib.pyplot.show.

type out_file:

str | None

returns:

Displays or saves the Matplotlib figure.

rtype:

None

See also

snapatac2.ex.export_coverage

Export coverage tracks for genome browsers.

Examples

>>> import snapatac2 as snap
>>> adata = snap.read(snap.datasets.pbmc5k(type="h5ad"))
>>> snap.pl.coverage(
...     adata,
...     region="chr1:100000-200000",
...     groupby="cell_type",
...     out_file="coverage.png",
... )
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