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)