scib_metrics.clisi_knn

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scib_metrics.clisi_knn#

scib_metrics.clisi_knn(X, labels, perplexity=None, scale=True)[source]#

Compute the cell-type local inverse simpson index (cLISI) for each cell [Korsunsky et al., 2019].

Returns a scaled version of the cLISI score for each cell, by default [Luecken et al., 2022].

Parameters:

  • X (NeighborsResults) – A NeighborsResults object.

  • labels (ndarray) – Array of shape (n_cells,) representing cell type label values for each cell.

  • perplexity (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:

float

Returns:

clisi cLISI score.

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