I just
updated
the phytools function reroot
so that the default
position
along the edge at which to re-root the tree is at the
node.number
node supplied by the user. Previously, the function
would not run when position
was not supplied.
E.g.:
library(phytools)
plotTree(tree,offset=0.8)
nodelabels()
tiplabels()
Now, let's perform operations on this original tree:
## reroot 0.1 along edge leading to node 22
t_22<-reroot(tree,node.number=22,position=0.1)
plotTree(t_22)
## reroot halfway along edge leading to tip "D"
node<-which(tree$tip.label=="D")
position<-0.5*tree$edge.length[which(tree$edge[,2]==node)]
t_D<-reroot(tree,node,position)
plotTree(t_D)
## reroot at node 16
t_16<-reroot(tree,16)
plotTree(t_16)
## reroot at tip "A"
plotTree(t_A<-reroot(tree,which(tree$tip.label=="A")))
Note that in this function the argument position
is the
distance from the rootward end of the edge leading to node
node.number
at which the tree should be re-rooted. Also,
though it is hard to demonstrate here, the function now has an
interactive=TRUE
mode (described
here).
No comments:
Post a Comment
Note: due to the very large amount of spam, all comments are now automatically submitted for moderation.