as.phylo {ape} | R Documentation |
as.phylo
is a generic function which converts an object into a
tree of class "phylo"
. There are currently two methods for this
generic for objects of class "hclust"
and of class
"phylog"
(implemented in the package ade4).
as.hclust.phylo
is a method of the generic
as.hclust
which converts an object of class
"phylo"
into one of class "hclust"
. This can used to
convert an object of class "phylo"
into one of class
"dendrogram"
(see examples).
as.phylo(x, ...) ## S3 method for class 'hclust': as.phylo(x, ...) ## S3 method for class 'phylog': as.phylo(x, ...) ## S3 method for class 'phylo': as.hclust(x, ...)
x |
an object to be converted into another class. |
... |
further arguments to be passed to or from other methods. |
An object of class "hclust"
or "phylo"
.
Emmanuel Paradis paradis@isem.univ-montp2.fr
hclust
, as.hclust
,
dendrogram
, phylog
data(bird.orders) hc <- as.hclust(bird.orders) tr <- as.phylo(hc) identical(bird.orders, tr) # FALSE, but... all.equal(bird.orders, tr) # ... TRUE ### shows the three plots for tree objects: dend <- as.dendrogram(hc) layout(matrix(c(1:3, 3), 2, 2)) plot(bird.orders, font = 1) plot(hc) par(mar = c(8, 0, 0, 0)) # leave space for the labels plot(dend) ### how to get (nearly) identical plots with ### plot.phylo and plot.dendrogram: layout(matrix(1:2, 2, 1)) plot(bird.orders, font = 1, no.margin = TRUE) par(mar = c(0, 0, 0, 8)) plot((dend), horiz = TRUE) layout(matrix(1, 1, 1))