greedyModularityCut {conos}R Documentation

Performs a greedy top-down selective cut to optmize modularity

Description

Performs a greedy top-down selective cut to optmize modularity

Usage

greedyModularityCut(
  wt,
  N,
  leaf.labels = NULL,
  minsize = 0,
  minbreadth = 0,
  flat.cut = TRUE
)

Arguments

wt

walktrap result

N

numeric Number of top greedy splits to take

leaf.labels

leaf sample label factor, for breadth calculations - must be a named factor containing all wt$names, or if wt$names is null, a factor listing cells in the same order as wt leafs (default=NULL)

minsize

numeric Minimum size of the branch (in number of leafs) (default=0)

minbreadth

numeric Minimum allowed breadth of a branch (measured as normalized entropy) (default=0)

flat.cut

boolean Whether to simply take a flat cut (i.e. follow provided tree; default=TRUE). Does no observe minsize/minbreadth restrictions

Value

list(hclust - hclust structure of the derived tree, leafContent - binary matrix with rows corresponding to old leaves, columns to new ones, deltaM - modularity increments)


[Package conos version 1.4.2 Index]