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Quality Control Filter (SpatialCellData)

Source: R/process.R
QCFilter.Rd

Removes cells that fail quality control criteria based on cell area and/or total marker intensity.

Usage

QCFilter(
  object,
  min_area = NULL,
  max_area = NULL,
  min_intensity = 0,
  max_intensity = NULL
)

Arguments

object

An SpatialCellData-class object.

min_area

Numeric or NULL. Minimum cell area.

max_area

Numeric or NULL. Maximum cell area.

min_intensity

Numeric. Minimum total marker intensity. Default 0.

max_intensity

Numeric or NULL. Maximum total marker intensity.

Value

A filtered SpatialCellData-class object.

Examples

counts <- matrix(rnorm(60, 5), nrow = 20,
                 dimnames = list(NULL, c("CD3", "CD8", "CD20")))
coords <- data.frame(x = runif(20), y = runif(20))
meta <- data.frame(cell_id = 1:20, sample_id = "s1",
                   cell_area = c(5, seq(50, 200, length.out = 18), 5000))
obj <- CreateSpatialObject(counts, coords, meta)
filtered <- QCFilter(obj, min_area = 10, max_area = 1000)
NCells(filtered)
#> [1] 18