Plot contour lines.

Usage

plotContour(
  spe,
  coi = NULL,
  overlay = c("cell", "density", "none"),
  id = "cell_type",
  sub.level = NULL,
  line.type = 1,
  line.width = 0.5,
  line.alpha = 1,
  ...
)

Arguments

spe: A SpatialExperiment object.
coi: A character vector of cell types of interest (COIs). All cell types are chosen if NULL or 'overall'.
overlay: Character vector. Options are 'cell' (plot overlay on cells), 'density' (overlay on density), or 'none'. Default to 'cell'.
id: A character. The name of the column of colData(spe) containing the cell type identifiers. Set to 'cell_type' by default.
sub.level: Character vector. Subset on specific level.
line.type: shape of contour. See 'ggplot2::geom_path()'.
line.width: size of contour.
line.alpha: alpha of contour between 0 and 1.
...: Aesthetic mappings to pass to 'plotSpatial()' or 'plotDensity()', depending on the overlay.

Value

A ggplot object.

Examples


data("xenium_bc_spe")

spe <- gridDensity(spe)

coi <- "Breast cancer"

spe <- getContour(spe, coi = coi)
#> Using bins = 10 to draw contours with equal cell numbers.

plotContour(spe, coi = coi, line.width = 0.3, pt.alpha = 0.2)