tacco.tools.annotate_novosparc

annotate_novosparc(adata, reference, annotation_key=None, counts_location=None, position_key=('x', 'y'), alpha=1.0, reads=False)[source]

Annotates an AnnData using reference data by NovoSpaRc [Nitzan19].

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 key where the annotation is 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().

  • position_key – The .obsm key or array-like of .obs keys with the position space coordinates. If alpha==1, this is not referenced.

  • alpha – The alpha parameter of NovoSpaRc.

  • reads – Whether to reduce the mapping to types using the counts per reference observation as weights or just flat weights per cell.

Returns:

Returns the annotation in a DataFrame.