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

Usage

plotCellCompo(
  spe,
  coi,
  id = "cell_type",
  level.name = paste0(janitor::make_clean_names(coi), "_contour"),
  by.roi = FALSE,
  all = TRUE
)

Arguments

spe: A SpatialExperiment object.
coi: A character vector of cell types of interest (COIs).
id: A character. The name of the column of colData(spe) containing the cell type identifiers. Set to cell_type by default.
level.name: The column name that generated by cellAssign.
by.roi: Logical. Default is FALSE, set to TRUE to allow plotting by ROI.
all: Logical. Whether to include all the cell types in the plot. Default to TRUE. If FALSE, the cell types specified in 'coi' will not be included in the plot.

Value

A ggplot object.

Examples


data("xenium_bc_spe")
spe <- gridDensity(spe, coi = c("Breast cancer", "Fibroblasts"))
spe <- findROI(spe, coi = c("Breast cancer", "Fibroblasts"))
spe <- getContour(spe, coi = "Breast cancer")
#> Using bins = 10 to draw contours.
spe <- allocateCells(spe)
#> Assigning cells to ROIs defined by Breast cancer, Fibroblasts 
#> Assigning cells to contour levels of Breast cancer 
#> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
plotCellCompo(spe, coi = "Breast cancer")

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