a character string giving the method used to create the
labels. Three choices are possible: "number" (the default),
"md5sum", and "user", or any unambiguous abbreviation
of these.
prefix
the prefix used if method = "number".
nodeList
a named list specifying how nodes are names if
method = "user" (see details and examples).
...
further arguments passed to grep.
Details
The three methods are described below:
“number”The labels are created with 1, 2, ... prefixed
with the argument prefix; thus the default is to have
Node1, Node2, ... Set prefix = "" to have only numbers.
“md5sum”For each node, the labels of the tips descendant
from this node are extracted, sorted alphabetically, and written
into a temporary file, then the md5sum of this file is extracted
and used as label. This results in a 32-character string which is
unique (even accross trees) for a given set of tip labels.
“user”the argument nodeList must be a list with
names, the latter will be used as node labels. For each element of
nodeList, the tip labels of the tree are searched for
patterns present in this element: this is done using
grep. Then the most recent common ancestor of
the matching tips is given the corresponding names as labels. This
is repeated for each element of nodeList.
The method "user" can be used in combination with either of the
two others (see examples). Note that this method only modifies the
specified node labels (so that if the other nodes have already labels
they are not modified) while the two others change all labels.
Value
an object of class "phylo".
Author(s)
Emmanuel Paradis
See Also
makeLabel, grep,
mixedFontLabel, label2table
Examples
tr <-
"((Pan_paniscus,Pan_troglodytes),((Homo_sapiens,Homo_erectus),Homo_abilis));"
tr <- read.tree(text = tr)
tr <- makeNodeLabel(tr, "u", nodeList = list(Pan = "Pan", Homo = "Homo"))
plot(tr, show.node.label = TRUE)
### does not erase the previous node labels:
tr <- makeNodeLabel(tr, "u", nodeList = list(Hominid = c("Pan","Homo")))
plot(tr, show.node.label = TRUE)
### the two previous commands could be combined:
L <- list(Pan = "Pan", Homo = "Homo", Hominid = c("Pan","Homo"))
tr <- makeNodeLabel(tr, "u", nodeList = L)
### combining different methods:
tr <- makeNodeLabel(tr, c("n", "u"), prefix = "#", nodeList = list(Hominid = c("Pan","Homo")))
plot(tr, show.node.label = TRUE)