doSNNCluster

Cluster cells using a SNN cluster approach.

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

Value

giotto object with new clusters appended to cell metadata

Details

See sNNclust from dbscan package