louvain_k: Optimizes Louvain clustering over a range of number of...

In califano-lab/PISCES: Protein Activity Inferecne in Single Cells

Optimizes Louvain clustering over a range of number of neighbors 'k' by silhouette score.

Description

Optimizes Louvain clustering over a range of number of neighbors 'k' by silhouette score.

Usage

louvain_k(dist.mat, kmin = 5, kmax = 50, kstep = 5)

Arguments

dist.mat	Distance matrix or distance structure like that generated by 'dist'.
kmin	Minimum number of neighbors Default of 5.
kmax	Maximum number of neibhbors Default of 50.
kstep	Step size between k values. Default of 5.

Value

A list; 'opt.clust' with the optimal clustering; 'clustering.objs', a list of all clusterings generated; 'sil.scores' a list of silhouette scores for each clustering object.

califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.