scvelo.pp.normalize_per_cell

scvelo.pp.normalize_per_cell(data, counts_per_cell_after=None, counts_per_cell=None, key_n_counts=None, max_proportion_per_cell=None, use_initial_size=True, layers=None, enforce=None, copy=False)

Normalize each cell by total counts over all genes.

Parameters:

  • data (AnnData, np.ndarray, sp.sparse) – The (annotated) data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

  • counts_per_cell_after (float or None, optional (default: None)) – If None, after normalization, each cell has a total count equal to the median of the counts_per_cell before normalization.

  • counts_per_cell (np.array, optional (default: None)) – Precomputed counts per cell.

  • key_n_counts (str, optional (default: ‘n_counts’)) – Name of the field in adata.obs where the total counts per cell are stored.

  • max_proportion_per_cell (int (default: None)) – Exclude genes counts that account for more than a specific proportion of cell size, e.g. 0.05.

  • use_initial_size (bool (default: True)) – Whether to use initial cell sizes oder actual cell sizes.

  • layers (str or list (default: [‘spliced’, ‘unspliced’])) – Keys for layers to be also considered for normalization.

  • copy (bool, optional (default: False)) – If an AnnData is passed, determines whether a copy is returned.

Return type:

Returns or updates adata with normalized counts.