Plot cell type composition in each density level of cell of interest.

Usage

plotCellCompo(
  spe,
  contour = NULL,
  id = "cell_type",
  by.roi = FALSE,
  self.included = TRUE
)

Arguments

spe: A SpatialExperiment object.
contour: A character vector of cell type(s) on which the contour density level is calculated. If NULL, it looks for 'overall_contour' in colData(spe). Default to NULL.
id: A character. The name of the column of colData(spe) containing the cell type identifiers. Set to 'cell_type' by default.
by.roi: Logical. Default is FALSE, set to TRUE to allow plotting by ROI.
self.included: Logical. Whether to include all the cell types in the plot. Default to TRUE. If FALSE, the cell types specified in 'contour' will not be included in the plot.

Value

A ggplot object.

Examples


data("xenium_bc_spe")
coi <- "Breast cancer"
spe <- gridDensity(spe, coi = coi)
spe <- findROI(spe, coi = coi)
spe <- getContour(spe, coi = coi)
#> Using bins = 10 to draw contours with equal cell numbers.
spe <- allocateCells(spe, contour = coi)
#> Assigning cells to ROIs defined by Breast cancer 
#> Assigning cells to contour levels of Breast cancer 
plotCellCompo(spe, contour = "Breast cancer")

plotCellCompo(spe, contour = "Breast cancer", by.roi = TRUE)