doSNNCluster | R Documentation |
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
)
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 |
See sNNclust
from dbscan package
giotto object with new clusters appended to cell metadata
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