mantispy.tl.similarity#

mantispy.tl.similarity(adata, metric='cosine', use_rep=None, key_added='similarity', copy=False)[source]#

Store pairwise profile similarity in obsp[key_added].

Parameters:

adata AnnData: Profiles to compare.
metric str (default: 'cosine'): Similarity between profiles, one of METRICS.
use_rep str | None (default: None): Compare obsm[use_rep] instead of X.
key_added str (default: 'similarity'): obsp key written.
copy bool (default: False): Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes the dense float32 similarity matrix of similarity_matrix to obsp[key_added].

Notes

The result is dense and quadratic in the number of profiles, so this expects well- or perturbation-level profiles rather than single cells.