Wrapper to calculate imhomogenous K function between a cell and surrounding types on each image

Calculate the imhomogenous K function (a measure of cell type abundance) for each cell to other cell types

Usage

getAbundances(
  cells,
  r = 200,
  distFun = "abundance",
  redDimName = "abundances",
  cellType = "cellType",
  imageID = "imageID",
  spatialCoords = c("x", "y"),
  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
r: Radius to include in that calculation of pairwise abundance (K-function) between cells (can be a numeric or vector of radii)
distFun: What distance function to use.
redDimName: Name of the reduced dimension to store in sce.
cellType: The name of the column in colData that stores the cell types.
imageID: The name of the column in colData that Stores the image ids.
spatialCoords: The names of the columns in colData that store the spatial coordinates.
nCores: Number of cores for parallel processing

Examples

library(dplyr)
data("kerenSCE")

singleCellDataCounts <- getAbundances(kerenSCE,
  r = 200,
)