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).
old2new.phylo
and new2old.phylo
are utility functions
for converting between the old and new coding of the class
"phylo"
.
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, ...) old2new.phylo(phy) new2old.phylo(phy)
x |
an object to be converted into another class. |
... |
further arguments to be passed to or from other methods. |
phy |
an object of class "phylo" . |
An object of class "hclust"
or "phylo"
.
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
hclust
, as.hclust
,
dendrogram
, phylog
,
as.phylo.formula
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))