scib_metrics.ilisi_knn#
- scib_metrics.ilisi_knn(X, batches, perplexity=None, scale=True)[source]#
Compute the integration local inverse simpson index (iLISI) for each cell [Korsunsky et al., 2019].
Returns a scaled version of the iLISI score for each cell, by default [Luecken et al., 2022].
- Parameters:
X (
NeighborsResults
) – ANeighborsResults
object.batches (
ndarray
) – Array of shape (n_cells,) representing batch values for each cell.perplexity (
Optional
[float
] (default:None
)) – Parameter controlling effective neighborhood size. If None, the perplexity is set to the number of neighbors // 3.scale (
bool
(default:True
)) – Scale lisi into the range [0, 1]. If True, higher values are better.
- Return type:
- Returns:
ilisi iLISI score.