doSNNCluster#
Last Updated: Jan 14, 2025
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#
|
giotto object |
|
name for cluster, default to “sNN_clus” |
|
type of NN network to use (only works on kNN), default to “kNN” |
|
name of kNN network to use, default to “kNN.pca” |
|
Neighborhood size for nearest neighbor sparsification to create the shared NN graph, default = 20 |
|
Two objects are only reachable from each other if they share at least eps nearest neighbors, default = 4 |
|
minimum number of points that share at least eps nearest neighbors for a point to be considered a core points, default = 16 |
|
should borderPoints be assigned to clusters like in DBSCAN? (default = TRUE) |
|
boolean: return giotto object (default = TRUE) |
|
set seed (default = FALSE) |
|
number for seed |
Details#
See sNNclust
from dbscan package
Value#
giotto object with new clusters appended to cell metadata