Phenotype Summary (SpatialCellData)

Computes phenotype counts and proportions per sample.

Usage

PhenotypeSummary(object)

Arguments

object

An SpatialCellData-class object.

Value

A data frame with columns sample_id, phenotype, count, and proportion.

Examples

counts <- matrix(c(rnorm(15, 5), rnorm(15, 1)), ncol = 2,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(15), y = runif(15))
obj <- CreateSpatialObject(counts, coords)
obj <- PhenotypeCells(obj, thresholds = list(CD3 = 3, CD8 = 3))
PhenotypeSummary(obj)
#>   sample_id phenotype count proportion
#> 1   sample1      CD3+    15          1