https://github.com/cran/ape
Tip revision: 73dd5a0622c43e3b0ec4b74c5955453d095bc623 authored by Emmanuel Paradis on 01 October 2013, 00:00:00 UTC
version 3.0-11
version 3.0-11
Tip revision: 73dd5a0
plot.phylo.R
## plot.phylo.R (2013-09-10)
## Plot Phylogenies
## Copyright 2002-2013 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 = TRUE, rotate.tree = 0,
open.angle = 0, node.depth = 1, ...)
{
Ntip <- length(x$tip.label)
if (Ntip < 2) {
warning("found less than 2 tips in the tree")
return(NULL)
}
if (any(tabulate(x$edge[, 1]) == 1))
stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
.nodeHeight <- function(Ntip, Nnode, edge, Nedge, yy)
.C(node_height, as.integer(Ntip), as.integer(Nnode),
as.integer(edge[, 1]), as.integer(edge[, 2]),
as.integer(Nedge), as.double(yy),
DUP = FALSE)[[6]]
.nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth)
.C(node_depth, as.integer(Ntip), as.integer(Nnode),
as.integer(edge[, 1]), as.integer(edge[, 2]),
as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth),
DUP = FALSE)[[6]]
.nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
.C(node_depth_edgelength, as.integer(Ntip),
as.integer(Nnode), as.integer(edge[, 1]),
as.integer(edge[, 2]), as.integer(Nedge),
as.double(edge.length), double(Ntip + Nnode),
DUP = FALSE)[[7]]
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
if (any(x$edge < 1) || any(x$edge > Ntip + Nnode))
stop("tree badly conformed; cannot plot. Check the edge matrix.")
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
"unrooted", "radial"))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length)) use.edge.length <- FALSE
## the order of the last two conditions is important:
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge) root.edge <- FALSE
if (type == "fan" && root.edge) {
warning("drawing root edge with type = 'fan' is not yet supported")
root.edge <- FALSE
}
phyloORclado <- type %in% c("phylogram", "cladogram")
horizontal <- direction %in% c("rightwards", "leftwards")
xe <- x$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") {
x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
if (!identical(x$edge, xe)) {
## modified from Li-San Wang's fix (2007-01-23):
ereorder <- match(x$edge[, 2], xe[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
}
}
### By contrats to ape (< 2.4), the arguments edge.color, etc., are
### not elongated before being passed to segments(), except if needed
### to be reordered
yy <- numeric(Ntip + Nnode)
TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
## 'z' is the tree in postorder order used in calls to .C
z <- reorder(x, order = "postorder")
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
if (type == "cladogram" && !use.edge.length) node.pos <- 2
}
if (node.pos == 1)
yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
else {
## node_height_clado requires the number of descendants
## for each node, so we compute `xx' at the same time
ans <- .C(node_height_clado, as.integer(Ntip),
as.integer(Nnode), as.integer(z$edge[, 1]),
as.integer(z$edge[, 2]), as.integer(Nedge),
double(Ntip + Nnode), as.double(yy),
DUP = FALSE)
xx <- ans[[6]] - 1
yy <- ans[[7]]
}
if (!use.edge.length) {
if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth) - 1
xx <- max(xx) - xx
} else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
} else {
twopi <- 2 * pi
rotate.tree <- twopi * 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
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
xx <- seq(0, twopi * (1 - 1/Ntip) - twopi * open.angle/360,
length.out = Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
if (use.edge.length) {
r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
} else {
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
r <- 1/r
}
theta <- theta + rotate.tree
xx <- r * cos(theta)
yy <- r * sin(theta)
}, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
XY <- if (use.edge.length)
unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree)
else
unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp, 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])
}, "radial" = {
X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
X[X == 1] <- 0
## radius:
X <- 1 - X/Ntip
## angle (1st compute the angles for the tips):
yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode))
Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
xx <- X * cos(Y + rotate.tree)
yy <- X * sin(Y + rotate.tree)
})}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp - min(tmp) + 1
}
if (root.edge) {
if (direction == "rightwards") xx <- xx + x$root.edge
if (direction == "upwards") yy <- yy + x$root.edge
}
}
if (no.margin) par(mai = rep(0, 4))
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
x.lim <- c(0, NA)
pin1 <- par("pin")[1] # width of the device in inches
strWi <- strwidth(x$tip.label, "inches") # id. for the tip labels
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
xx.tips <- xx[1:Ntip] * 1.04
## 'alp' is the conversion coefficient from
## user coordinates to inches:
alp <- try(uniroot(function(a) max(a*xx.tips + strWi) - pin1,
c(0, 1e6))$root, silent = TRUE)
## if the above fails, give 1/3 of the device for the tip labels:
if (is.character(alp)) tmp <- max(xx.tips)*1.5 else {
tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
}
x.lim[2] <- tmp
} else x.lim <- c(1, Ntip)
} else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(min(xx) - offset, max(xx) + offset)
} else x.lim <- c(min(xx), max(xx))
}, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
}, "radial" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
})
} else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal) x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
x.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
if (type == "radial")
x.lim[1] <-
if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
else -1
}
## mirror the xx:
if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal) y.lim <- c(1, Ntip) else {
y.lim <- c(0, NA)
pin2 <- par("pin")[2] # height of the device in inches
strWi <- strwidth(x$tip.label, "inches")
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
yy.tips <- yy[1:Ntip] * 1.04
## 'alp' is the conversion coefficient from
## user coordinates to inches:
alp <- try(uniroot(function(a) max(a*yy.tips + strWi) - pin2,
c(0, 1e6))$root, silent = TRUE)
## if the above fails, give 1/3 of the device for the tip labels:
if (is.character(alp)) tmp <- max(yy.tips)*1.5 else {
tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
}
y.lim[2] <- tmp
}
} else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
}, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
}, "radial" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
})
} else if (length(y.lim) == 1) {
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$tip.label) * 0.018 * max(yy) * cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
}
## mirror the yy:
if (phyloORclado && direction == "downwards") yy <- 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.default(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
ylab = "", axes = FALSE, asp = asp, ...)
if (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards") 1 else 0
if (phyloORclado && show.tip.label) {
MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
##xx <- xx + MAXSTRING
}
if (!horizontal) {
psr <- par("usr")
MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
##yy <- yy + MAXSTRING
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
horizontal, edge.color, edge.width, edge.lty)
} else {
if (type == "fan") {
ereorder <- match(z$edge[, 2], x$edge[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
circular.plot(z$edge, Ntip, Nnode, xx, yy, theta,
r, edge.color, edge.width, edge.lty)
} else
cladogram.plot(x$edge, xx, yy, edge.color, edge.width, edge.lty)
}
if (root.edge)
switch(direction,
"rightwards" = segments(0, yy[ROOT], x$root.edge, yy[ROOT]),
"leftwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT]),
"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$tip.label)
if (phyloORclado)
text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label, adj = adj,
font = font, srt = srt, cex = cex, col = tip.color)
if (type == "unrooted") {
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(XY$axe) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] * 1.05
sel <- abs(XY$axe) > pi/4 & abs(XY$axe) < 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(XY$axe)[sel] / pi - 0.5)
sel <- XY$axe > pi / 4 & XY$axe < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel] / 2
sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex,
x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
} else { # if lab4ut == "axial"
adj <- abs(XY$axe) > pi/2
srt <- 180 * XY$axe / pi
srt[adj] <- srt[adj] - 180
adj <- as.numeric(adj)
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(XY$axe)
yy.tips <- yy.tips + label.offset * sin(XY$axe)
}
## `srt' takes only a single value, so can't vectorize this:
## (and need to 'elongate' these vectors:)
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip)
text(xx.tips[i], yy.tips[i], cex = cex[i],
x$tip.label[i], adj = adj[i], font = font[i],
srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
angle <- atan2(yy.tips, xx.tips) # in radians
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
s <- xx.tips < 0
angle <- angle * 180/pi # switch to degrees
angle[s] <- angle[s] + 180
adj <- as.numeric(s)
## `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.tips[i], yy.tips[i], x$tip.label[i], font = font[i],
cex = cex[i], srt = angle[i], adj = adj[i],
col = tip.color[i])
}
}
if (show.node.label)
text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
x$node.label, adj = adj, font = font, srt = srt, cex = cex)
}
L <- list(type = type, use.edge.length = use.edge.length,
node.pos = node.pos, node.depth = node.depth,
show.tip.label = show.tip.label,
show.node.label = show.node.label, font = font,
cex = cex, adj = adj, srt = srt, no.margin = no.margin,
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 = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
invisible(L)
}
phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
edge.color, edge.width, edge.lty)
{
nodes <- (Ntip + 1):(Ntip + Nnode)
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp
}
## 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:
NodeInEdge1 <- vector("list", Nnode)
for (i in nodes) {
ii <- i - Ntip
j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
tmp <- range(yy[edge[j, 2]])
y0v[ii] <- tmp[1]
y1v[ii] <- tmp[2]
}
## ... et un trait horizontal partant de chaque tip et chaque noeud
## vers la racine
x0h <- xx[edge[, 1]]
x1h <- xx[edge[, 2]]
y0h <- yy[edge[, 2]]
nc <- length(edge.color)
nw <- length(edge.width)
nl <- length(edge.lty)
if (nc + nw + nl == 3) {
color.v <- edge.color
width.v <- edge.width
lty.v <- edge.lty
} else {
Nedge <- dim(edge)[1]
edge.color <- rep(edge.color, length.out = Nedge)
edge.width <- rep(edge.width, length.out = Nedge)
edge.lty <- rep(edge.lty, length.out = Nedge)
DF <- data.frame(edge.color, edge.width, edge.lty, stringsAsFactors = FALSE)
color.v <- rep("black", Nnode)
width.v <- rep(1, Nnode)
lty.v <- rep(1, Nnode)
for (i in 1:Nnode) {
br <- NodeInEdge1[[i]]
if (length(br) > 2) {
x <- unique(DF[br, 1])
if (length(x) == 1) color.v[i] <- x
x <- unique(DF[br, 2])
if (length(x) == 1) width.v[i] <- x
x <- unique(DF[br, 3])
if (length(x) == 1) lty.v[i] <- x
} else {
A <- br[1]
B <- br[2]
if (any(DF[A, ] != DF[B, ])) {
color.v[i] <- edge.color[B]
width.v[i] <- edge.width[B]
lty.v[i] <- edge.lty[B]
## add a new line:
y0v <- c(y0v, y0v[i])
y1v <- c(y1v, yy[i + Ntip])
x0v <- c(x0v, x0v[i])
color.v <- c(color.v, edge.color[A])
width.v <- c(width.v, edge.width[A])
lty.v <- c(lty.v, edge.lty[A])
## shorten the line:
y0v[i] <- yy[i + Ntip]
} else {
color.v[i] <- edge.color[A]
width.v[i] <- edge.width[A]
lty.v[i] <- edge.lty[A]
}
}
}
}
if (horizontal) {
segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws horizontal lines
segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v, lty = lty.v) # draws vertical lines
} else {
segments(y0h, x0h, y0h, x1h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws vertical lines
segments(y0v, x0v, y1v, x0v, col = color.v, lwd = width.v, lty = lty.v) # draws horizontal lines
}
}
cladogram.plot <- function(edge, xx, yy, edge.color, edge.width, edge.lty)
segments(xx[edge[, 1]], yy[edge[, 1]], xx[edge[, 2]], yy[edge[, 2]],
col = edge.color, lwd = edge.width, lty = edge.lty)
circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta,
r, edge.color, edge.width, edge.lty)
### 'edge' must be in postorder order
{
r0 <- r[edge[, 1]]
r1 <- r[edge[, 2]]
theta0 <- theta[edge[, 2]]
costheta0 <- cos(theta0)
sintheta0 <- sin(theta0)
x0 <- r0 * costheta0
y0 <- r0 * sintheta0
x1 <- r1 * costheta0
y1 <- r1 * sintheta0
segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width, lty = edge.lty)
tmp <- which(diff(edge[, 1]) != 0)
start <- c(1, tmp + 1)
Nedge <- dim(edge)[1]
end <- c(tmp, Nedge)
## function dispatching the features to the arcs
foo <- function(edge.feat, default) {
if (length(edge.feat) == 1) return(rep(edge.feat, Nnode))
else {
edge.feat <- rep(edge.feat, length.out = Nedge)
feat.arc <- rep(default, Nnode)
for (k in 1:Nnode) {
tmp <- edge.feat[start[k]]
if (tmp == edge.feat[end[k]]) feat.arc[k] <- tmp
}
}
feat.arc
}
co <- foo(edge.color, "black")
lw <- foo(edge.width, 1)
ly <- foo(edge.lty, 1)
for (k in 1:Nnode) {
i <- start[k]
j <- end[k]
X <- rep(r[edge[i, 1]], 100)
Y <- seq(theta[edge[i, 2]], theta[edge[j, 2]], length.out = 100)
lines(X*cos(Y), X*sin(Y), col = co[k], lwd = lw[k], lty = ly[k])
}
}
unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree)
{
foo <- function(node, ANGLE, AXIS) {
ind <- which(edge[, 1] == node)
sons <- edge[ind, 2]
start <- AXIS - ANGLE/2
for (i in 1:length(sons)) {
h <- edge.length[ind[i]]
angle[sons[i]] <<- alpha <- ANGLE*nb.sp[sons[i]]/nb.sp[node]
axis[sons[i]] <<- beta <- start + alpha/2
start <- start + alpha
xx[sons[i]] <<- h*cos(beta) + xx[node]
yy[sons[i]] <<- h*sin(beta) + yy[node]
}
for (i in sons)
if (i > Ntip) foo(i, angle[i], axis[i])
}
Nedge <- dim(edge)[1]
yy <- xx <- numeric(Ntip + Nnode)
## `angle': the angle allocated to each node wrt their nb of tips
## `axis': the axis of each branch
axis <- angle <- numeric(Ntip + Nnode)
## start with the root...
foo(Ntip + 1L, 2*pi, 0 + rotate.tree)
M <- cbind(xx, yy)
axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
axeGTpi <- axe > pi
## insures that returned angles are in [-PI, +PI]:
axe[axeGTpi] <- axe[axeGTpi] - 2*pi
list(M = M, axe = axe)
}
node.depth <- function(phy, method = 1)
{
n <- length(phy$tip.label)
m <- phy$Nnode
N <- dim(phy$edge)[1]
phy <- reorder(phy, order = "postorder")
.C(node_depth, as.integer(n), as.integer(m),
as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
as.integer(N), double(n + m), as.integer(method),
DUP = FALSE)[[6]]
}
node.depth.edgelength <- function(phy)
{
n <- length(phy$tip.label)
m <- phy$Nnode
N <- dim(phy$edge)[1]
phy <- reorder(phy, order = "postorder")
.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$edge.length), double(n + m),
DUP = FALSE)[[7]]
}
node.height <- function(phy, clado.style = FALSE)
{
n <- length(phy$tip.label)
m <- phy$Nnode
N <- dim(phy$edge)[1]
phy <- reorder(phy)
yy <- numeric(n + m)
e2 <- phy$edge[, 2]
yy[e2[e2 <= n]] <- 1:n
phy <- reorder(phy, order = "postorder")
e1 <- phy$edge[, 1]
e2 <- phy$edge[, 2]
if (clado.style)
.C(node_height_clado, as.integer(n), as.integer(m),
as.integer(e1), as.integer(e2), as.integer(N),
double(n + m), as.double(yy), DUP = FALSE)[[7]]
else
.C(node_height, as.integer(n), as.integer(m),
as.integer(e1), as.integer(e2), as.integer(N),
as.double(yy), DUP = FALSE)[[6]]
}
node.height.clado <- function(phy)
{
warning("the function 'node.height.clado' will be removed soon.\nUse node.height(phy, clado.style = TRUE) instead.")
node.height(phy, TRUE)
}
plot.multiPhylo <- function(x, layout = 1, ...)
{
layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
if (!devAskNewPage() && interactive()) {
devAskNewPage(TRUE)
on.exit(devAskNewPage(FALSE))
}
for (i in 1:length(x)) plot(x[[i]], ...)
}
trex <- function(phy, title = TRUE, subbg = "lightyellow3",
return.tree = FALSE, ...)
{
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
devmain <- dev.cur() # where the main tree is plotted
restore <- function() {
dev.set(devmain)
assign("last_plot.phylo", lastPP, envir = .PlotPhyloEnv)
}
on.exit(restore())
NEW <- TRUE
cat("Click close to a node. Right-click to exit.\n")
repeat {
x <- identify.phylo(phy, quiet = TRUE)
if (is.null(x)) return(invisible(NULL)) else {
x <- x$nodes
if (is.null(x)) cat("Try again!\n") else {
if (NEW) {
dev.new()
par(bg = subbg)
devsub <- dev.cur()
NEW <- FALSE
} else dev.set(devsub)
tr <- extract.clade(phy, x)
plot(tr, ...)
if (is.character(title)) title(title)
else if (title) {
tl <-
if (is.null(phy$node.label))
paste("From node #", x, sep = "")
else paste("From", phy$node.label[x - Ntip(phy)])
title(tl)
}
if (return.tree) return(tr)
restore()
}
}
}
}
kronoviz <- function(x, layout = length(x), horiz = TRUE, ...)
{
par(mar = rep(0.5, 4), oma = rep(2, 4))
rts <- sapply(x, function(x) branching.times(x)[1])
maxrts <- max(rts)
lim <- cbind(rts - maxrts, rts)
Ntree <- length(x)
Ntips <- sapply(x, Ntip)
if (horiz) {
nrow <- layout
w <- 1
h <- Ntips
} else {
nrow <- 1
w <- Ntips
h <- 1
}
layout(matrix(1:layout, nrow), widths = w, heights = h)
if (layout < Ntree && !devAskNewPage() && interactive()) {
devAskNewPage(TRUE)
on.exit(devAskNewPage(FALSE))
}
if (horiz) {
for (i in 1:Ntree)
plot(x[[i]], x.lim = lim[i, ], ...)
} else {
for (i in 1:Ntree)
plot(x[[i]], y.lim = lim[i, ], direction = "u", ...)
}
axisPhylo(if (horiz) 1 else 4) # better if the deepest tree is last ;)
}