spac.transformations.batch_normalize(adata, annotation, output_layer, input_layer=None, method='median', log=False)[source]

Adjust the features of every marker using a normalization method.

The normalization methods are summarized here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723144/

Parameters:

  • adata (anndata.AnnData) – The AnnData object.

  • annotation (str) – The name of the annotation in adata to define batches.

  • output_layer (str) – The name of the new layer to add to the anndata object for storing normalized data.

  • input_layer (str, optional) – The name of the layer from which to read data. If None, read from .X.

  • method ({"median", "Q50", "Q75", "z-score"}, default "median") – The normalization method to use.

  • log (bool, default False) – If True, take the log2 of features before normalization. Ensure this is boolean.