mantispy.tl.percent_replicating#

mantispy.tl.percent_replicating(adata, groupby='Metadata_Perturbation', metric='pearson', use_rep=None, null_size=10000, quantile=0.95, seed=0, key_added='percent_replicating', copy=False)[source]#

Median replicate correlation against a non-replicate null.

An older readout, largely replaced by mAP. It thresholds rather than ranks, and it depends on the number of replicates per perturbation. It is included because many published results report it.

Parameters:
adata AnnData

Well-level profiles with several replicates per group.

groupby str (default: 'Metadata_Perturbation')

Column whose groups are the replicate sets.

metric str (default: 'pearson')

Similarity between profiles, one of METRICS.

use_rep str | None (default: None)

Score obsm[use_rep] instead of X.

null_size int (default: 10000)

Number of draws in the non-replicate null.

quantile float (default: 0.95)

Quantile of the null medians a group has to beat to count as replicating.

seed int (default: 0)

Seed for the null draws.

key_added str (default: 'percent_replicating')

Name for the outputs.

copy bool (default: False)

Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes uns["mantispy"][key_added] with group, n_replicates, median_replicate_correlation, null_threshold and is_significant (whether the group replicates above the null), leaving out groups with a single replicate. Writes uns["mantispy"][key_added + "_summary"] with fraction_replicating and n_groups.