Phenotype Cells by Marker Thresholds — phenotype

Assigns phenotype labels to cells based on marker intensity thresholds. A cell is considered positive for a marker if its intensity exceeds the given threshold.

Usage

phenotype_cells(dt, thresholds, labels = NULL)

Arguments

dt: A data.table as returned by read_spatial() or normalise_markers().
thresholds: A named list where names are marker column names and values are numeric thresholds. Example: list(CD3 = 0.5, CD8 = 0.3).
labels: A named character vector mapping phenotype signatures to labels, or NULL for automatic labelling. When NULL, phenotypes are labelled by concatenating positive marker names with "+".

Value

The input data.table with an added phenotype column.

Examples

dt <- data.table::data.table(
  sample_id = "s1", cell_id = 1:6,
  x = runif(6), y = runif(6),
  CD3 = c(0.8, 0.1, 0.9, 0.2, 0.7, 0.05),
  CD8 = c(0.1, 0.6, 0.7, 0.05, 0.8, 0.02)
)
result <- phenotype_cells(dt, thresholds = list(CD3 = 0.5, CD8 = 0.5))
table(result$phenotype)
#> 
#>      CD3+ CD3+/CD8+      CD8+  Negative 
#>         1         2         1         2