compute_simpson_index: Compute the Local Inverse Simpson Index (LISI)

In immunogenomics/LISI: Local Inverse Simpson Index (LISI) for scRNAseq data

Description

Compute the Local Inverse Simpson Index (LISI)

Usage

compute_simpson_index(
  D,
  knn_idx,
  batch_labels,
  n_batches,
  perplexity = 15,
  tol = 1e-05
)

Arguments

D	Distance matrix of K nearest neighbors.
knn_idx	Adjacency matrix of K nearest neighbors.
batch_labels	A categorical variable.
n_batches	The number of categories in the categorical variable.
perplexity	The effective number of neighbors around each cell.
tol	Stop when the score converges to this tolerance.

immunogenomics/LISI documentation built on July 30, 2020, 5:49 a.m.