doSNNCluster: doSNNCluster

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Cluster cells using a SNN cluster approach.

Usage

doSNNCluster(
  gobject,
  name = "sNN_clus",
  nn_network_to_use = "kNN",
  network_name = "kNN.pca",
  k = 20,
  eps = 4,
  minPts = 16,
  borderPoints = TRUE,
  return_gobject = TRUE,
  set_seed = F,
  seed_number = 1234
)

Arguments

gobject	giotto object
name	name for cluster
nn_network_to_use	type of NN network to use (only works on kNN)
network_name	name of kNN network to use
k	Neighborhood size for nearest neighbor sparsification to create the shared NN graph.
eps	Two objects are only reachable from each other if they share at least eps nearest neighbors.
minPts	minimum number of points that share at least eps nearest neighbors for a point to be considered a core points.
borderPoints	should borderPoints be assigned to clusters like in DBSCAN?
return_gobject	boolean: return giotto object (default = TRUE)
set_seed	set seed
seed_number	number for seed

Details

See sNNclust from dbscan package

Value

giotto object with new clusters appended to cell metadata

Examples

    doSNNCluster(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.