-## plot.phylo.R (2010-03-15)
+## plot.phylo.R (2011-02-11)
## Plot Phylogenies
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2011 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
}
x.lim[2] <- tmp
- if (direction == "leftwards") xx <- x.lim[2] - xx #max(xx[ROOT] + tmp)
-# else max(xx[1:Ntip] + tmp)
} else x.lim <- c(1, Ntip)
} else switch(type, "fan" = {
if (show.tip.label) {
if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
else -1
}
+ ## mirror the xx:
+ if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal) y.lim <- c(1, Ntip) else {
tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
}
y.lim[2] <- tmp
- if (direction == "downwards") yy <- y.lim[2] - yy
}
} else switch(type, "fan" = {
if (show.tip.label) {
if (type == "radial")
y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
}
+ ## mirror the yy:
+ if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy
if (phyloORclado && root.edge) {
if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
}
- asp <- if (type %in% c("fan", "radial")) 1 else NA # fix by Klaus Schliep (2008-03-28)
+ asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards") 1 else 0
"upwards" = segments(xx[ROOT], 0, xx[ROOT], x$root.edge),
"downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge))
if (show.tip.label) {
+ if (is.expression(x$tip.label)) underscore <- TRUE
if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado)
srt <- 180*XY$axe/pi
srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
## `srt' takes only a single value, so can't vectorize this:
+ ## (and need to 'elongate' these vectors:)
+ font <- rep(font, length.out = Ntip)
+ tip.color <- rep(tip.color, length.out = Ntip)
+ cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip)
- text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
- font = font, srt = srt[i], col = tip.color[i])
+ text(xx[i], yy[i], cex = cex[i], x$tip.label[i], adj = adj[i],
+ font = font[i], srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
adj <- numeric(Ntip)
adj[xx.tips < 0] <- 1
## `srt' takes only a single value, so can't vectorize this:
+ ## (and need to 'elongate' these vectors:)
+ font <- rep(font, length.out = Ntip)
+ tip.color <- rep(tip.color, length.out = Ntip)
+ cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip)
- text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
+ text(xx[i], yy[i], x$tip.label[i], font = font[i], cex = cex[i],
srt = angle[i], adj = adj[i], col = tip.color[i])
}
}