rotate: Swapping Sister Clades

In ape: Analyses of Phylogenetics and Evolution

Swapping Sister Clades

Description

For a given node, rotate exchanges the position of two clades descending from this node. It can handle dichotomies as well as polytomies. In the latter case, two clades from the polytomy are selected for swapping.

rotateConstr rotates internal branches giving a constraint on the order of the tips.

Usage

rotate(phy, node, polytom = c(1, 2))
rotateConstr(phy, constraint)

Arguments

phy	an object of class "phylo".
node	a vector of mode numeric or character specifying the number of the node.
polytom	a vector of mode numeric and length two specifying the two clades that should be exchanged in a polytomy.
constraint	a vector of mode character specifying the order of the tips as they should appear when plotting the tree (from bottom to top).

Details

phy can be either rooted or unrooted, contain polytomies and lack branch lengths. In the presence of very short branch lengths it is convenient to plot the phylogenetic tree without branch lengths in order to identify the number of the node in question.

node can be any of the interior nodes of a phylogenetic tree including the root node. Number of the nodes can be identified by the nodelabels function. Alternatively, you can specify a vector of length two that contains either the number or the names of two tips that coalesce in the node of interest.

If the node subtends a polytomy, any two clades of the the polytomy can be chosen by polytom. On a plotted phylogeny, the clades are numbered from bottom to top and polytom is used to index the two clades one likes to swop.

Value

an object of class "phylo".

Author(s)

Christoph Heibl [e-mail], Emmanuel Paradis

See Also

plot.phylo, nodelabels, root, drop.tip

Examples

# create a random tree:
tre <- rtree(25)

# visualize labels of internal nodes:
plot(tre, use.edge.length=FALSE)
nodelabels()

# rotate clades around node 30:
tre.new <- rotate(tre, 30)

# compare the results:
par(mfrow=c(1,2)) # split graphical device
plot(tre) # plot old tre
plot(tre.new) # plot new tree

# visualize labels of terminal nodes:
plot(tre)
tiplabels()

# rotate clades containing nodes 12 and 20:
tre.new <- rotate(tre, c(12, 21))

# compare the results:
par(mfrow=c(1,2)) # split graphical device
plot(tre) # plot old tre
plot(tre.new) # plot new tree

# or you migth just specify tiplabel names:
tre.new <- rotate(tre, c("t3", "t14"))

# compare the results:
par(mfrow=c(1,2)) # devide graphical device
plot(tre) # plot old tre
plot(tre.new) # plot new tree

# a simple example for rotateConstr:
A <- read.tree(text = "((A,B),(C,D));")
B <- read.tree(text = "(((D,C),B),A);")
B <- rotateConstr(B, A$tip.label)
plot(A); plot(B, d = "l")

# something more interesting (from ?cophyloplot):
tr1 <- rtree(40)
## drop 20 randomly chosen tips:
tr2 <- drop.tip(tr1, sample(tr1$tip.label, size = 20))
## rotate the root and reorder the whole:
tr2 <- rotate(tr2, 21)
tr2 <- read.tree(text = write.tree(tr2))
X <- cbind(tr2$tip.label, tr2$tip.label) # association matrix
cophyloplot(tr1, tr2, assoc = X, space = 28)
## before reordering tr2 we have to find the constraint:
co <- tr2$tip.label[order(match(tr2$tip.label, tr1$tip.label))]
newtr2 <- rotateConstr(tr2, co)
cophyloplot(tr1, newtr2, assoc = X, space = 28)

ape documentation built on May 29, 2024, 10:50 a.m.