new_clustering: Louvain/leiden clustering with optimal KNN structure

In renjun0324/KKLClustering: Large-scale single-cell clustering algorithm based on optimal KNN graph structure

Louvain/leiden clustering with optimal KNN structure

Description

This function is used to run Louvain clustering with optimal KNN graph structure

Usage

new_clustering(
  sampling_result = NULL,
  outlier_kmeans = NULL,
  assess_index = "Calinski_Harabasz",
  cluster_method = "louvain",
  res_range = seq(0.2, 3, 0.2),
  is_weight = TRUE,
  python_path = "/usr/bin/python3",
  seed = 723
)

Arguments

sampling_result	sampling result from pre_partitioning function
outlier_kmeans	outlier detection result from OutlierKmeans function
assess_index	evaluation index used to select the optimal KNN graph structure
cluster_method	louvain or leiden
res_range	resolution range in clustering
python_path	python path to be used
seed	random seed

renjun0324/KKLClustering documentation built on Oct. 8, 2024, 7:39 p.m.