stream2.pp.normalize

stream2.pp.normalize(adata, method='lib_size', scale_factor=10000.0, save_raw=True)

Normalize count matrix.

Parameters:

• adata (AnnData) – Annotated data matrix.

• method (str, optional (default: ‘lib_size’)) –

  Choose from {{‘lib_size’,’tf_idf’}}. Method used for dimension reduction.

  ’lib_size’: Total-count normalize (library-size correct).

  ’tf_idf’: TF-IDF (term frequency–inverse document frequency)

  transformation.

Returns:

• updates adata with the following fields.

• X (numpy.ndarray (adata.X)) – Store #observations × #var_genes normalized data matrix.