Spatial Clusters (SpatialCellData)

Clusters cells based on spatial coordinates.

Usage

SpatialClusters(object, k, method = c("kmeans", "hierarchical"))

Arguments

object

An SpatialCellData-class object.

k

Integer. Number of clusters.

method

Character. "kmeans" (default) or "hierarchical".

Value

An SpatialCellData-class with a cluster column in meta_data.

Examples

counts <- matrix(rnorm(100), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(
  x = c(rnorm(25, 0, 5), rnorm(25, 50, 5)),
  y = c(rnorm(25, 0, 5), rnorm(25, 50, 5)))
obj <- CreateSpatialObject(counts, coords)
obj <- SpatialClusters(obj, k = 2)
table(Meta(obj)$cluster)
#> 
#>  1  2 
#> 25 25