Expression-Based Cell Clustering

Clusters cells based on marker expression profiles.

Usage

ExpressionClusters(
  object,
  k,
  method = c("kmeans", "hierarchical"),
  slot = "data",
  markers = NULL
)

Arguments

object

An SpatialCellData-class object.

k

Integer. Number of clusters.

method

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

slot

Character. "data" (default) or "counts".

markers

Character vector or NULL. Markers to use.

Value

An SpatialCellData-class with an expr_cluster column in meta_data.

Examples

counts <- matrix(c(rnorm(50, 10), rnorm(50, 0)), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(50), y = runif(50))
obj <- CreateSpatialObject(counts, coords)
obj <- ExpressionClusters(obj, k = 2)
table(Meta(obj)$expr_cluster)
#> 
#>  1  2 
#> 25 25