tacco.tools.annotate_nnls

annotate_nnls(adata, reference, annotation_key=None, counts_location=None)[source]

Annotates an AnnData using reference data by NNLS (non-negative least squares).

This is the direct interface to this annotation method. In practice using the general wrapper annotate() is recommended due to its higher flexibility.

Parameters:

  • adata – An AnnData including expression data in .X.

  • reference – Reference data to get the annotation definition from.

  • annotation_key – The .obs and/or .varm key where the annotation and/or profiles are stored in the reference. If None, it is inferred from reference, if possible.

  • counts_location – A string or tuple specifying where the count matrix is stored, e.g. ‘X’, (‘raw’,’X’), (‘raw’,’obsm’,’my_counts_key’), (‘layer’,’my_counts_key’), … For details see counts().

Returns:

Returns the annotation in a DataFrame.