-## plot.phylo.R (2011-03-23)
+## plot.phylo.R (2012-03-22)
## Plot Phylogenies
-## Copyright 2002-2011 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
- node.pos = NULL, show.tip.label = TRUE,
- show.node.label = FALSE, edge.color = "black",
- edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
- adj = NULL, srt = 0, no.margin = FALSE,
- root.edge = FALSE, label.offset = 0, underscore = FALSE,
- x.lim = NULL, y.lim = NULL, direction = "rightwards",
- lab4ut = "horizontal", tip.color = "black", ...)
+plot.phylo <-
+ function(x, type = "phylogram", use.edge.length = TRUE,
+ node.pos = NULL, show.tip.label = TRUE,
+ show.node.label = FALSE, edge.color = "black",
+ edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
+ adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
+ label.offset = 0, underscore = FALSE, x.lim = NULL,
+ y.lim = NULL, direction = "rightwards", lab4ut = "horizontal",
+ tip.color = "black", plot = TRUE, rotate.tree = 0, ...)
{
Ntip <- length(x$tip.label)
if (Ntip == 1) {
}
## 'z' is the tree in pruningwise order used in calls to .C
z <- reorder(x, order = "pruningwise")
-### edge.color <- rep(edge.color, length.out = Nedge)
-### edge.width <- rep(edge.width, length.out = Nedge)
-### edge.lty <- rep(edge.lty, length.out = Nedge)
-### ## fix from Li-San Wang (2007-01-23):
-### xe <- x$edge
-### x <- reorder(x, order = "pruningwise")
-### ereorder <- match(x$edge[, 2], xe[, 2])
-### edge.color <- edge.color[ereorder]
-### edge.width <- edge.width[ereorder]
-### edge.lty <- edge.lty[ereorder]
-### ## end of fix
+
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
} else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
- } else switch(type, "fan" = {
+ } else {
+ rotate.tree <- 2 * pi * rotate.tree/360
+ switch(type, "fan" = {
## if the tips are not in the same order in tip.label
## and in edge[, 2], we must reorder the angles: we
## use `xx' to store temporarily the angles
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
r <- 1/r
}
+ theta <- theta + rotate.tree
xx <- r*cos(theta)
yy <- r*sin(theta)
}, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length)
- unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp)
+ unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree)
else
- unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp)
+ unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp, rotate.tree)
## rescale so that we have only positive values
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
## angle (1st compute the angles for the tips):
yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
- xx <- X * cos(Y)
- yy <- X * sin(Y)
- })
+ xx <- X * cos(Y + rotate.tree)
+ yy <- X * sin(Y + rotate.tree)
+ })}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal) y.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
- y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
+ y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
if (type == "radial")
- y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
+ y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
}
## mirror the yy:
- if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy
+ if (phyloORclado && direction == "downwards") yy <- max(yy) - 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", "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 (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards") 1 else 0
if (phyloORclado && show.tip.label) {
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
- #xx <- xx + MAXSTRING
+ ##xx <- xx + MAXSTRING
}
if (!horizontal) {
psr <- par("usr")
if (show.node.label)
text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
x$node.label, adj = adj, font = font, srt = srt, cex = cex)
+}
L <- list(type = type, use.edge.length = use.edge.length,
node.pos = node.pos, show.tip.label = show.tip.label,
show.node.label = show.node.label, font = font,
}
}
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
+unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree)
{
foo <- function(node, ANGLE, AXIS) {
ind <- which(edge[, 1] == node)
yy[sons[i]] <<- h*sin(beta) + yy[node]
}
for (i in sons)
- if (i > Ntip) foo(i, angle[i], axis[i])
+ if (i > Ntip) foo(i, angle[i], axis[i])
}
Nedge <- dim(edge)[1]
yy <- xx <- numeric(Ntip + Nnode)
## `axis': the axis of each branch
axis <- angle <- numeric(Ntip + Nnode)
## start with the root...
- foo(Ntip + 1L, 2*pi, 0)
+ foo(Ntip + 1L, 2*pi, 0 + rotate.tree)
M <- cbind(xx, yy)
axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
projects / ape.git / blobdiff