Get contour from density
Usage
getContour(
spe,
coi = NULL,
equal.cell = FALSE,
bins = NULL,
binwidth = NULL,
breaks = NULL,
id = "cell_type"
)Arguments
- spe
A SpatialExperiment object.
- coi
A character vector of cell types of interest (COIs).
- equal.cell
Logical. Whether to use produce contour levels so that there are roughly the same number of cells of the COI at each level.
- bins
An integer. Number of contour levels.
- binwidth
A numeric scale of the smoothing bandwidth.
- breaks
A numeric scale referring to the breaks in
ggplot2:::contour_breaks.- id
A character. The name of the column of colData(spe) containing the cell type identifiers. Set to cell_type by default. Only needed when
equal.cell = TRUE.
Value
A SpatialExperiment object. An sf object of the contour region of the specified level is stored in the metadata of the SpatialExperiment object.
Examples
data("xenium_bc_spe")
spe <- gridDensity(spe)
coi <- "Breast cancer"
spe <- getContour(spe, coi = coi)
#> Using bins = 10 to draw contours.