Perform kernel density estimation on SpatialExperiment

Usage

computeDensity(
  spe,
  mode = c("pixels", "points"),
  kernel = c("gaussian", "epanechnikov", "quartic", "disc"),
  bandwidth = NULL,
  weights = NULL,
  ngrid.x = NULL,
  ngrid.y = NULL,
  grid.length.x = 100,
  grid.length.y = NULL,
  xlim = NULL,
  ylim = NULL,
  diggle = FALSE
)

Arguments

spe: A SpatialExperiment object.
mode: Choose either points or pixels. Specifying whether to compute the density at a grid pixel location or at at point.
kernel: The smoothing kernel. Options are gaussian, epanechnikov, quartic or disc.
bandwidth: The smoothing bandwidth. By default performing automatic bandwidth selection using cross-validation using function spatstat.explore::bw.diggle.
weights: Optional weights to be attached to the points.
ngrid.x: Number of grids in the x-direction.
ngrid.y: Number of grids in the y-direction.
grid.length.x: Grid length in the x-direction. Default to 100 (micron).
grid.length.y: Grid length in the y-direction.
xlim: The range of the x-coordinates of the image.
ylim: The range of the y-coordinates of the image.
diggle: Logical. If TRUE, use the Jones-Diggle improved edge correction. See spatstat.explore::density.ppp() for details.

Value

Output from spatstat.explore::density.ppp.