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