Collapse branches under a tolerance level

Source: R/unbranch.R

Collapse branches under a tolerance level

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)
#> 
#> Attaching package: ‘ape’
#> The following objects are masked from ‘package:dendextend’:
#> 
#>     ladderize, rotate
dend %>%
  as.phylo() %>%
  di2multi(tol = 0.2) %>%
  plot(main = "phylo")