evaluate_emd: Evaluate Earth Mover's Distance

View source: R/evaluate_performance.R

evaluate_emdR Documentation

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()


biosurf/cyCombine documentation built on May 23, 2024, 4:07 a.m.