Leiden clustering on bigraph

This function takes a caclust object with precomputed SNN-graph and clusters cells and genes simultaneously.

Usage

run_leiden(
  caclust,
  resolution = 1,
  n.int = 10,
  rand_seed = 2358,
  cast_to_dense = TRUE,
  leiden_pack = "igraph"
)

Arguments

caclust

caclust object with SNN calculated.

resolution

float number. Resolution for leiden algorithm.

n.int

Integer. Number of iterations for leiden algorithm.

rand_seed

integer. Random seed.

cast_to_dense

logical. Casting sparse SNN adjacency matrix to dense speeds up the leiden algorithm.

leiden_pack

character. Optional values are 'igraph'(default) and 'leiden', the package used for leiden clustering.

Value

Object of type "caclust" with cell and gene clusters saved.

See also

Other biclustering: caclust, make_SNN(), run_spectral()