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 variable for dataset Which dimensionally reduced space to use Dimensions to use Neighbor number to examine per group Maximum size of local neighborhood to compute Error bound on the neighbor finding algorithm (from RANN) Displays progress bar

## Value

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