R: Collapse branches under a tolerance level

collapse_branch {dendextend} | R Documentation

## 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")

[Package dendextend version 1.8.0 Index]