After quantile normalization, users can additionally run the Louvain algorithm for community detection, which is widely used in single-cell analysis and excels at merging small clusters into broad cell classes.
object with refined cluster assignment updated in
"louvain_cluster" variable in cellMeta slot. Can be fetched
with object$louvain_cluster
liger object. Should run quantile_norm before calling.
The maximum number of nearest neighbours to compute. (default 20)
Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities. (default 1.0)
Sets the cutoff for acceptable Jaccard index when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 --- no pruning, 1 --- prune everything). (default 1/15)
The error bound of the nearest neighbor search. (default 0.1)
Number of random starts. (default 10)
Maximal number of iterations per random start. (default 100)
Seed of the random number generator. (default 1)
Print messages (TRUE by default)
Indices of factors to use for clustering. Default NULL
uses all available factors.
rliger-deprecated