Remove excessive number of neighbours in a knn graph

Ensure that each cell's number of neighbours does not exceed a cutoff

Usage

CutKnn(
  object,
  graph.name,
  new.graph = NULL,
  k.max,
  assay = NULL,
  verbose = TRUE
)

Arguments

object

A Seurat object

graph.name

name of a Graph or Neighbor instance stored in the Seurat object.

new.graph

name of the trimmed graph to save in the Seurat object

k.max

maximum number of neigbours allowed per cell

assay

name of the assay to use. Ignored when graph object is a Neighbor object. If not specified (default), the default assay is used

verbose

whether to print messages. Set to FALSE to disable

Value

the Seurat object with a new Graph or Neighbor instance