Swapping Sister Clades
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.
rotate(phy, node, polytom = c(1, 2)) rotateConstr(phy, constraint)
phy |
an object of class |
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). |
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.
an object of class "phylo".
Christoph Heibl heibl@lmu.de, Emmanuel Paradis
# 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.