compute_emd: Compute EMD

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

Compute EMD

Description

Given a dataframe, the Earth Movers Distance is computed, using the emdist package. A matrix is returned containing the EMD for each marker for each group of cells.

Usage

compute_emd(
  df,
  binSize = 0.1,
  cell_col = "label",
  batch_col = "batch",
  markers = NULL
)

Arguments

df	Dataframe to compute the EMD of
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

See Also

Other emd: evaluate_emd()

Examples

## Not run: 
emd <- compute_emd(df, markers = markers)

## End(Not run)

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