evaluate_emd: Evaluate Earth Mover's Distance

In shdam/cyCombine: Robust integration of single-cell cytometry datasets within and across technologies

Evaluate Earth Mover's Distance

Description

The function computes the Earth Mover's Distance of the two given datasets. Then the reduction is calculated as the relative change in total EMD.

Usage

evaluate_emd(
  uncorrected,
  corrected,
  binSize = 0.1,
  cell_col = "label",
  batch_col = "batch",
  markers = NULL,
  plots = TRUE,
  filter_limit = 2
)

Arguments

uncorrected	Dataframe of uncorrected data
corrected	Dataframe of corrected data
binSize	The size of bins to use when binning data
cell_col	Column name of df that contains cell population labels (or clusters)
batch_col	Column name of df that contains batch numbers
markers	Vector of the markers to calculate EMD for. If NULL, get_markers will be used to find markers
plots	If TRUE, a violin and scatter plot of the emds will be returned
filter_limit	Limit for EMD removal (Removing EMDs that are below filter_limit in both before and after correction)

See Also

Other emd: compute_emd()

shdam/cyCombine documentation built on June 12, 2022, 11:29 p.m.