-## 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)
}