mantispy.pp.well_qc

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mantispy.pp.well_qc#

mantispy.pp.well_qc(adata, min_cells=50, max_nan_fraction=0.1, max_control_cv=None, key='selected', copy=False)#

Flag wells with too few cells, too much missing data, or unstable controls.

Parameters:

  • adata (AnnData) – Single-cell object to summarize per well.

  • min_cells (int (default: 50)) – Wells with fewer cells than this fail.

  • max_nan_fraction (float (default: 0.1)) – Wells missing more than this fraction of their values fail.

  • max_control_cv (float | None (default: None)) – For control wells only, the largest acceptable median coefficient of variation across features. None skips the check, which is the default because a sensible value depends on the assay.

  • key (str | None (default: 'selected')) – Restrict the statistics to features flagged by this boolean var column.

  • copy (bool (default: False)) – Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes uns["mantispy"]["well_qc"], a frame with the columns Metadata_Plate, Metadata_Well, n_cells, nan_fraction, control_cv and qc_well_pass, and broadcasts obs["qc_well_pass"].

Notes

The table keeps plate and well as columns because a MultiIndex in uns cannot be written to h5ad.

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