mantispy.tl.map

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mantispy.tl.map#

mantispy.tl.map(adata, pos_sameby=None, pos_diffby=(), neg_sameby=(), neg_diffby=(), mode=None, annotation_key=None, reference='negcon', use_rep=None, null_size=10000, threshold=0.05, seed=0, distance='cosine', key_added='map', copy=False)[source]#

Mean average precision per group, with a permutation null.

Parameters:

  • adata (AnnData) – Profiles to score, normally well-level.

  • pos_sameby (Sequence[str] | None (default: None)) – obs columns a positive pair must share, in copairs’ terms. Pass the four pair arguments or mode, not both.

  • pos_diffby (Sequence[str] (default: ())) – obs columns in which a positive pair must differ.

  • neg_sameby (Sequence[str] (default: ())) – obs columns a negative pair must share.

  • neg_diffby (Sequence[str] (default: ())) – obs columns in which a negative pair must differ.

  • mode (str | None (default: None)) –

    A preset for the pair definitions, one of the following.

    "activity"

    Is this perturbation distinguishable from the negative controls? Its replicates are retrieved against control profiles only. This is the phenotypic activity of Kalinin et al. (2025), the number published JUMP results quote. Needs reference.

    "consistency"

    Do perturbations sharing an annotation look more alike than those that do not? This is the phenotypic consistency of Kalinin et al. Needs annotation_key (a mechanism, target or gene column) and is meant for consensus profiles of perturbations already known to be active.

    "replicability"

    Do a perturbation’s replicates retrieve each other against all other profiles? The mAP-nonrep of the batch-correction benchmark of Arevalo et al. (2024).

    "cross_plate"

    As "replicability", but a replicate counts only if it is on a different plate, which separates reproducible biology from plate effects.

  • annotation_key (str | None (default: None)) – The obs column mode="consistency" groups by.

  • reference (str | None (default: 'negcon')) – Which rows are the negative controls for mode="activity", either "negcon" or the name of a boolean obs column.

  • use_rep (str | None (default: None)) – Score obsm[use_rep] instead of X.

  • null_size (int (default: 10000)) – Size of the permutation null.

  • threshold (float (default: 0.05)) – Significance threshold passed to copairs.

  • seed (int (default: 0)) – Seed for the permutation null.

  • distance (str (default: 'cosine')) – Distance copairs ranks by.

  • key_added (str (default: 'map')) – Where to store results.

  • 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 per-group table to uns["mantispy"][key_added] and joins obs[key_added] and obs[key_added + "_qvalue"] back onto the rows.

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