-## plot.phylo.R (2010-03-15)
+## plot.phylo.R (2010-03-19)
## Plot Phylogenies
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
"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)