Wrapper to calculate pairwise distance between cell types by image

Calculates the euclidean distance from each cell to the nearest cell of each type

Usage

getDistances(
  cells,
  maxDist = NULL,
  imageID = "imageID",
  spatialCoords = c("x", "y"),
  cellType = "cellType",
  redDimName = "distances",
  distFun = "min",
  nCores = 1
)

Arguments

cells

A dataframe with a cellType column as well as x and y spatial coordinates. The dataframe must contain a imageID column and cellID (unique cell identifier's) column as well

maxDist

The maximum distance considered.

imageID

The name of the colData column that stores in the image ID.

spatialCoords

The columns that store the spatial coordinates.

cellType

The name of the colData column that stores the cell types.

redDimName

The name of the reduced dimension to store the distances in.

distFun

What distance function to use. Can be min or abundance.

nCores

Number of cores for parallel processing.

Examples

data("kerenSCE")

kerenSCE <- getDistances(kerenSCE,
  maxDist = 200
)