Here we compute a measure of how well mixed a composite dataset is. To compute, we first examine the local neighborhood for each cell (looking at max.k neighbors) and determine for each group (could be the dataset after integration) the k nearest neighbor and what rank that neighbor was in the overall neighborhood. We then take the median across all groups as the mixing metric per cell.

MixingMetric(
object,
grouping.var,
reduction = "pca",
dims = 1:2,
k = 5,
max.k = 300,
eps = 0,
verbose = TRUE
)

## Arguments

object

Seurat object

grouping.var

Grouping variable for dataset

reduction

Which dimensionally reduced space to use

dims

Dimensions to use

k

Neighbor number to examine per group

max.k

Maximum size of local neighborhood to compute

eps

Error bound on the neighbor finding algorithm (from RANN)

verbose

Displays progress bar

## Value

Returns a vector of values of the mixing metric for each cell