stereoAlign.metrics.lisi

stereoAlign.metrics.lisi(data: AnnData, key: str = 'batch', use_rep: str = 'X_umap', n_neighbors: int = 30)

Local inverse Simpson’s Index (LISI)

Calculate the Local inverse Simpson’s Index (LISI) metric of the data regarding a specific sample attribute and embedding. The LISI metric measures if cells from different samples mix well in their local neighborhood.

Parameters

data:

Data matrix with rows for cells and columns for genes.

key:

The sample attribute to be consider. Must exist in data.obs.

use_rep:

The embedding representation to be used. The key must be exist in data.obsm. By default, use UMAP coordinates.

n_neighbors:

Number of nearest neighbors.

Returns

lisi_mean:

Mean of calculated score.

lower:

Lower bound of 95% confidence interval.

upper:

Upper bound of 95% confidence interval.