-## plot.phylo.R (2009-11-10)
+## plot.phylo.R (2010-01-04)
## Plot Phylogenies
-## Copyright 2002-2009 Emmanuel Paradis
+## Copyright 2002-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
phyloORclado <- type %in% c("phylogram", "cladogram")
horizontal <- direction %in% c("rightwards", "leftwards")
+ xe <- x$edge # to save
if (phyloORclado) {
## we first compute the y-coordinates of the tips.
phyOrder <- attr(x, "order")
## make sure the tree is in cladewise order:
if (is.null(phyOrder) || phyOrder != "cladewise") {
- xe <- x$edge
x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
if (!identical(x$edge, xe)) {
## modified from Li-San Wang's fix (2007-01-23):
label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
direction = direction, tip.color = tip.color,
Ntip = Ntip, Nnode = Nnode)
- assign("last_plot.phylo", c(L, list(edge = x$edge, xx = xx, yy = yy)),
+ assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
invisible(L)
}
year = "2004",
volume = "20",
pages = "289-290",
-
+
textVersion = "Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.")
citFooter("As ape is evolving quickly, you may want to cite also its version number (found with 'library(help = ape)').")
\ No newline at end of file
\seealso{\code{\link{compar.lynch}}}
\examples{
### Example from Harvey and Pagel's book:
-\dontrun{
y<-c(10,8,3,4)
W <- matrix(c(1,1/6,1/6,1/6,1/6,1,1/2,1/2,1/6,1/2,1,1,1/6,1/2,1,1), 4)
compar.cheverud(y,W)
-}
### Example from Rohlf's 2001 article:
W<- matrix(c(
0,1,1,2,0,0,0,0,
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 \code{"phylo"}.
+}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
\code{\link{makeLabel}}, \code{\link[base]{grep}}