Phenotype Cells (SpatialCellData)

Assigns phenotype labels to cells based on marker intensity thresholds. Uses the normalised data slot.

Usage

PhenotypeCells(object, thresholds, labels = NULL)

Arguments

object

An SpatialCellData-class object.

thresholds

Named list of thresholds (marker name = value).

labels

Named character vector mapping signatures to labels, or NULL for automatic labelling.

Value

An SpatialCellData-class with a phenotype column in meta_data.

Examples

counts <- matrix(c(rnorm(10, 5), rnorm(10, 1)), ncol = 2,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(10), y = runif(10))
obj <- CreateSpatialObject(counts, coords)
obj <- PhenotypeCells(obj, thresholds = list(CD3 = 3, CD8 = 3))
table(Meta(obj)$phenotype)
#> 
#> CD3+ 
#>   10