scgenome.tl.sort_cells

scgenome.tl.sort_cells(adata, layer_name='copy', cell_ids=None, bin_ids=None, standarize=False)

Sort cells by hierarchical clustering on copy number values.

Parameters:

• adata (AnnData) – copy number data

• layer_name (str, optional) – layer with copy number data to use for sorting, None for X, by default ‘copy’

• cell_ids (str, optional) – subset of cells to cluster, by default None

• bin_ids (str, optional) – subset of bins to cluster, by default None

• standarize (bool) – standardize the data prior to sorting, by default False

Returns:

copy number data with cell_order column added to obs

Return type:

AnnData