Description Usage Arguments Value
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.
1 2 | MixingMetric(object, grouping.var, reduction = "pca", dims = 1:2,
k = 5, max.k = 300, eps = 0, verbose = TRUE)
|
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 |
Returns a vector of values representing the entropy metric from each bootstrapped iteration.
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