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Calculate batch LISI scores

rs_batch_lisi.Rd

Computes the Local Inverse Simpson's Index on batch labels using the kNN graph. Measures the effective number of batches in each cell's neighbourhood. Under perfect mixing LISI equals the number of batches, under no mixing LISI equals 1.

Usage

rs_batch_lisi(knn_mat, batch_vector)

Arguments

knn_mat

Integer matrix. The rows represent the cells and the columns the neighbour indices.

batch_vector

Integer vector. The integers indicate to which batch a given cell belongs.

Value

A list with the following items

  • per_cell - Per-cell LISI scores

  • mean_lisi - Mean LISI

  • median_lisi - Median LISI