Name regions by the cell types they are enriched for

The regions found by lisaClust() are numbered arbitrarily. nameRegions() gives each region the name of the marker cell type it is most enriched for, as measured by regionMap(type = "table"). Regions most enriched for the same marker get the same name, so several regions can be merged into one domain.

Usage

nameRegions(
  cells,
  markers,
  region = "region",
  cellType = "cellType",
  regionName = region
)

Arguments

cells

A SingleCellExperiment, SpatialExperiment or data frame with a region column.

markers

A character vector of cell types. Its names, when given, are used as the names of the regions; otherwise the cell types are.

region

The column storing the regions.

cellType

The column storing the cell types.

regionName

The output column for the named regions; by default the regions are replaced.

Value

cells with the named regions in the column regionName.

Examples

set.seed(51773)
x <- round(c(
  runif(200), runif(200) + 1, runif(200) + 2, runif(200) + 3,
  runif(200) + 3, runif(200) + 2, runif(200) + 1, runif(200)
), 4) * 100
y <- round(c(
  runif(200), runif(200) + 1, runif(200) + 2, runif(200) + 3,
  runif(200), runif(200) + 1, runif(200) + 2, runif(200) + 3
), 4) * 100
cellType <- factor(paste("c", rep(rep(c(1:2), rep(200, 2)), 4), sep = ""))
imageID <- rep(c("s1", "s2"), c(800, 800))
cells <- data.frame(x, y, cellType, imageID)
cells <- lisaClust(cells, k = 2)
#> Generating local indicators of spatial association.

cells <- nameRegions(cells, c(first = "c1", second = "c2"), regionName = "domain")
table(cells$domain, cells$cellType)
#>         
#>           c1  c2
#>   first  800   0
#>   second   0 800