-## plot.phylo.R (2011-06-14)
+## plot.phylo.R (2012-10-20)
## 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.
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, ...)
+ tip.color = "black", plot = TRUE, rotate.tree = 0, ...)
{
Ntip <- length(x$tip.label)
- if (Ntip == 1) {
- warning("found only one tip in the tree")
+ if (Ntip < 2) {
+ warning("found less than 2 tips in the tree")
return(NULL)
}
if (any(tabulate(x$edge[, 1]) == 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$root.edge
yy <- xx
xx <- tmp
}
- ## un trait vertical à chaque noeud...
+ ## un trait vertical a chaque noeud...
x0v <- xx[nodes]
y0v <- y1v <- numeric(Nnode)
## store the index of each node in the 1st column of edge:
}
}
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
+unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree)
{
foo <- function(node, ANGLE, AXIS) {
ind <- which(edge[, 1] == node)
yy[sons[i]] <<- h*sin(beta) + yy[node]
}
for (i in sons)
- if (i > Ntip) foo(i, angle[i], axis[i])
+ if (i > Ntip) foo(i, angle[i], axis[i])
}
Nedge <- dim(edge)[1]
yy <- xx <- numeric(Ntip + Nnode)
## `axis': the axis of each branch
axis <- angle <- numeric(Ntip + Nnode)
## start with the root...
- foo(Ntip + 1L, 2*pi, 0)
+ foo(Ntip + 1L, 2*pi, 0 + rotate.tree)
M <- cbind(xx, yy)
axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
as.integer(N), double(n + m), DUP = FALSE, PACKAGE = "ape")[[6]]
}
+node.depth.edgelength <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+ .C("node_depth_edgelength", as.integer(n), as.integer(n),
+ as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
+ as.integer(N), as.double(phy$edge.length), double(n + m),
+ DUP = FALSE, PACKAGE = "ape")[[7]]
+}
+
+node.height <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+
+ e1 <- phy$edge[, 1]
+ e2 <- phy$edge[, 2]
+
+ yy <- numeric(n + m)
+ TIPS <- e2[e2 <= n]
+ yy[TIPS] <- 1:n
+
+ .C("node_height", as.integer(n), as.integer(m),
+ as.integer(e1), as.integer(e2), as.integer(N),
+ as.double(yy), DUP = FALSE, PACKAGE = "ape")[[6]]
+}
+
+node.height.clado <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+
+ e1 <- phy$edge[, 1]
+ e2 <- phy$edge[, 2]
+
+ yy <- numeric(n + m)
+ TIPS <- e2[e2 <= n]
+ yy[TIPS] <- 1:n
+
+ .C("node_height_clado", as.integer(n), as.integer(m),
+ as.integer(e1), as.integer(e2), as.integer(N),
+ double(n + m), as.double(yy), DUP = FALSE,
+ PACKAGE = "ape")[[7]]
+}
+
plot.multiPhylo <- function(x, layout = 1, ...)
{
if (layout > 1)