Compute Cell Density — cell_density • phenoscapR

Estimates the local cell density around each cell using a circular neighbourhood of a given radius.

Usage

cell_density(dt, radius, target_phenotype = NULL)

Arguments

dt: A data.table with columns x and y.
radius: Numeric. Radius of the neighbourhood (in coordinate units).
target_phenotype: Character string or NULL. If provided, only cells of this phenotype are counted in the neighbourhood.

Value

The input data.table with an added density column representing the number of neighbours within the specified radius.

Examples

dt <- data.table::data.table(
  sample_id = "s1", cell_id = 1:50,
  x = runif(50, 0, 100), y = runif(50, 0, 100)
)
result <- cell_density(dt, radius = 20)
head(result[, .(cell_id, density)])
#>    cell_id density
#>      <int>   <num>
#> 1:       1       7
#> 2:       2       7
#> 3:       3       6
#> 4:       4       4
#> 5:       5       8
#> 6:       6       4