Plot ROIs on spatial.

Usage

plotROI(
  spe,
  roi = NULL,
  id = "cell_type",
  label = TRUE,
  show.legend = FALSE,
  reverseY = NULL,
  ...
)

Arguments

spe: A SpatialExperiment object.
roi: Character. The name of the group or cell type on which the roi is computed. All cell types are chosen if NULL or 'overall'.
id: Character. The name of the column of colData(spe) containing the cell type identifiers. Set to cell_type by default.
label: Logical. Show ROI label or not.
show.legend: Logical. Show legend or not.
reverseY: Logical. Whether to reverse Y coordinates. Default is TRUE if the spe contains an image (even if not plotted) and FALSE if otherwise.
...: Parameters pass to plotSpatial

Value

A ggplot object.

Examples


data("xenium_bc_spe")

coi <- c("Breast cancer", "Fibroblasts")

spe <- gridDensity(spe, coi = coi)

spe <- findROI(spe, coi = coi, method = "walktrap", steps = 5)

plotROI(spe, roi = coi, pt.size = 0.3, pt.alpha = 0.2)