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feat: more functionality for coverage plot#479

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feat: more functionality for coverage plot#479
Cmfffff wants to merge 1 commit into
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@Cmfffff

@Cmfffff Cmfffff commented Jul 10, 2026

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Hi Kaihang,

I've been using SnapATAC2 to analyze my scATAC-seq data for quite some time.

I noticed that the latest version of the repository introduces the coverage function, which provides a convenient way to quickly visualize genomic tracks. I really like this feature.

I added a few enhancements to improve its functionality, and I thought others in the community might find them useful as well. Here's the resulting plot:

plotting.coverage(
    data,
    region="DIP2C", 
    groupby="group",
    gene_annotation="gencode.gtf",
    gene_type="protein_coding"
    highlight=[
        (610_000, 635_000, "tab:orange"),
        (645_000, 665_000, "tab:blue")
    ],
    highlight_alpha=0.35,
    peak_track=True,
    out_file=str("coverage_test.png")
)
image

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