collapse_branch: Collapse branches under a tolerance level

In dendextend: Extending 'dendrogram' Functionality in R

Collapse branches under a tolerance level

Description

Collapse branches under a tolerance level

Usage

collapse_branch(dend, tol = 1e-08, lower = TRUE, ...)

Arguments

dend	dendrogram object
tol	a numeric value giving the tolerance to consider a branch length significantly greater than zero
lower	logical (TRUE). collapse branches which are lower than tol?
...	passed on (not used)

Value

A dendrogram with both of the root's branches of the same height

See Also

multi2di

Examples

# # ladderize is like sort(..., type = "node")
dend <- iris[1:5, -5] %>%
  dist() %>%
  hclust() %>%
  as.dendrogram()
par(mfrow = c(1, 3))
dend %>%
  ladderize() %>%
  plot(horiz = TRUE)
abline(v = .2, col = 2, lty = 2)
dend %>%
  collapse_branch(tol = 0.2) %>%
  ladderize() %>%
  plot(horiz = TRUE)
dend %>%
  collapse_branch(tol = 0.2) %>%
  ladderize() %>%
  hang.dendrogram(hang = 0) %>%
  plot(horiz = TRUE)

par(mfrow = c(1, 2))
dend %>%
  collapse_branch(tol = 0.2, lower = FALSE) %>%
  plot(horiz = TRUE, main = "dendrogram")
library(ape)
dend %>%
  as.phylo() %>%
  di2multi(tol = 0.2) %>%
  plot(main = "phylo")

dendextend documentation built on Oct. 13, 2024, 1:06 a.m.