scpdac.pp.bin_data

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scpdac.pp.bin_data#

scpdac.pp.bin_data(adata, n_bins=50, layer=None)#

Discretize expression values into n_bins per-cell quantile bins.

Thin, user-facing wrapper around the internal _bin_data routine. Safely handles dense arrays and sparse (csr/csc) matrices. The binned matrix is written to adata.layers["binned_data"] and bin edges to adata.obsm["bin_edges"].

Parameters:

  • adata (AnnData) – The input object (modified in place).

  • n_bins (int (default: 50)) – Number of bins. Defaults to 50, matching the packaged SCANVI models.

  • layer (str | None (default: None)) – Layer to bin; if None, adata.X is used.

Return type:

AnnData

Returns:

The same adata, with the binned layer attached (returned for chaining).

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