Plot contour lines. — plotContour • scider

Plot contour lines.

Usage

plotContour(
  spe,
  coi,
  overlay = c("cell", "density"),
  id = "cell_type",
  sub.level = NULL,
  ...
)

Arguments

spe: A SpatialExperiment object.
coi: A character vector of length 1 of the cell type of interest.
overlay: Character vector. Either plot overlay on density or cell. By default is 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.
...: Aesthetic mappings to pass to ggplot2::aes_string().

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.

plotContour(spe, coi = coi, size = 0.3, alpha = 0.2)