doSNNCluster#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L611

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 = FALSE,
  seed_number = 1234
)

Arguments#

Argument

Description

gobject

giotto object

name

name for cluster, default to “sNN_clus?

nn_network_to_use

type of NN network to use (only works on kNN), default to “kNN?

network_name

name of kNN network to use, default to “kNN.pca?

k

Neighborhood size for nearest neighbor sparsification to create the shared NN graph, default = 20

eps

Two objects are only reachable from each other if they share at least eps nearest neighbors, default = 4

minPts

minimum number of points that share at least eps nearest neighbors for a point to be considered a core points, default = 16

borderPoints

should borderPoints be assigned to clusters like in DBSCAN? (default = TRUE)

return_gobject

boolean: return giotto object (default = TRUE)

set_seed

set seed (default = FALSE)

seed_number

number for seed

Details#

See `sNNclust <#snnclust>`__ from dbscan package

Value#

giotto object with new clusters appended to cell metadata