Collapse branches under a tolerance level
Collapse branches under a tolerance level
collapse_branch(dend, tol = 1e-08, lower = TRUE, ...)
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) |
A dendrogram with both of the root's branches of the same height
# # 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")
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