tacco.tools.annotate_NMFreg

annotate_NMFreg(adata, reference, annotation_key, K=30, random_state=42, counts_location=None, min_counts_per_cell=0, min_counts_per_gene=0)[source]

Annotates an AnnData using reference data by NMFreg [Rodriques19].

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.

  • K – Number of NMF factors

  • random_state – Random seed

  • 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().

  • min_counts_per_cell – Minimum number of counts per cell

  • min_counts_per_gene – Minimum number of counts per gene

Returns:

Returns the annotation in a DataFrame.