Annotate all cells with contour level of cell type-specific density.

Annotate all cells with contour level of cell type-specific density.

Usage

allocateCells(spe, to.roi = TRUE, to.contour = TRUE, contour = NULL)

Arguments

spe

A SpatialExperiment object.

to.roi

Logical. Whether to allocate cells to ROIs.

to.contour

Logical. Whether to allocate cells to contour levels.

contour

Character. The name of the group or cell type on which the contour level is computed. If NULL, then the cell allocation will be performed for all detected contours. Default to NULL.

Value

A SpatialExperiment object. An extra column is added to the colData.

Examples

data("xenium_bc_spe")
spe <- gridDensity(spe)
coi <- "Breast cancer"
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 
#> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE