MixingMetric {Seurat}

Calculates a mixing metric

Description

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.

Usage

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