Local Structure Preservation Metric

Calculates the proportion of overlapping k-nearest neighbors between an original/reference embedding and an integrated/simulated embedding (adapted from Seurat LocalStruct and CellMixS locStructure).

Usage

calc_local_structure_metric(coords_pre, coords_post, k = 30)

Arguments

coords_pre

Matrix of coordinates before integration / reference (cells x dimensions).

coords_post

Matrix of coordinates after integration / simulated (cells x dimensions).

k

Number of nearest neighbors. Default is 30.

Value

A named list:

cell_overlaps

Numeric vector of overlap fractions per cell

mean_local_structure

Mean overlap fraction across cells (higher indicates better preservation)

median_local_structure

Median overlap fraction

Examples

coords <- matrix(stats::rnorm(100), 50, 2)
batch <- factor(rep(c("B1", "B2"), length.out = 50))
calc_local_structure_metric(coords, coords)
#> $cell_overlaps
#>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [39] 1 1 1 1 1 1 1 1 1 1 1 1
#> 
#> $mean_local_structure
#> [1] 1
#> 
#> $median_local_structure
#> [1] 1
#>