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|
## plot.phylo.R (2024-11-23)
## Plot Phylogenies
## Copyright 2002-2024 Emmanuel Paradis, 2021 Martin Smith, 2022 Damien de Vienne, 2024 Klaus Schliep
## colouring of segments by MS
## tidy trees by DdV
## 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 = NULL, edge.width = NULL, edge.lty = NULL,
node.color = NULL, node.width = NULL, node.lty = NULL,
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 = NULL,
tip.color = par("col"), plot = TRUE, rotate.tree = 0,
open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)
{
Ntip <- length(x$tip.label)
if (Ntip < 2) {
warning("found fewer than 2 tips in the tree")
return(NULL)
}
.nodeHeight <- function(edge, Nedge, yy)
.C(node_height, as.integer(edge[, 1]), as.integer(edge[, 2]),
as.integer(Nedge), as.double(yy))[[4]]
.nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth)
.C(node_depth, as.integer(Ntip),
as.integer(edge[, 1]), as.integer(edge[, 2]),
as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth))[[5]]
.nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
.C(node_depth_edgelength, as.integer(edge[, 1]),
as.integer(edge[, 2]), as.integer(Nedge),
as.double(edge.length), double(Ntip + Nnode))[[5]]
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
if (any(x$edge < 1) || any(x$edge > Ntip + Nnode))
stop("tree badly conformed; cannot plot. Check the edge matrix.")
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
"unrooted", "radial", "tidy"))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length)) {
use.edge.length <- FALSE
} else {
if (use.edge.length && type != "radial") {
tmp <- sum(is.na(x$edge.length))
if (tmp) {
warning(paste(tmp, "branch length(s) NA(s): branch lengths ignored in the plot"))
use.edge.length <- FALSE
}
}
}
if (is.numeric(align.tip.label)) {
align.tip.label.lty <- align.tip.label
align.tip.label <- TRUE
} else { # assumes is.logical(align.tip.labels) == TRUE
if (align.tip.label) align.tip.label.lty <- 3
}
if (align.tip.label) {
if (type %in% c("unrooted", "radial") || !use.edge.length || is.ultrametric(x))
align.tip.label <- FALSE
}
## the order of the last two conditions is important:
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge) root.edge <- FALSE
phyloORclado <- type %in% c("phylogram", "cladogram", "tidy")
horizontal <- direction %in% c("rightwards", "leftwards")
##tidy exception:
if (type == "tidy" && any(x$edge.length < 0))
stop("cannot plot in tidy mode with negative branch lengths. Check 'edge.length' vector.")
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$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
## TIDY
## Function to compute the size of labels
## for each tip in user coordinates
getStringLengthbyTip <- function(x, lab, sin, cex) {
s <- strwidth(lab, "inches", cex = cex)
lim <- getLimit(x, lab, sin, cex)
alp <- lim/sin
s*alp
}
### END TIDY
## Function to compute the axis limit
## x: vector of coordinates, must be positive (or at least the largest value)
## lab: vector of labels, length(x) == length(lab)
## sin: size of the device in inches
getLimit <- function(x, lab, sin, cex) {
s <- strwidth(lab, "inches", cex = cex) # width of the tip labels
## if at least one string is larger than the device,
## give 1/3 of the plot for the tip labels:
if (any(s > sin)) return(1.5 * max(x))
Limit <- 0
while (any(x > Limit)) {
i <- which.max(x)
## 'alp' is the conversion coeff from inches to user coordinates:
alp <- x[i]/(sin - s[i])
Limit <- x[i] + alp*s[i]
x <- x + alp*s
}
Limit
}
## 'z' is the tree in postorder order used in calls to .C
z <- reorder(x, order = "postorder")
if (phyloORclado) {
if (is.null(node.pos))
node.pos <-
if (type == "cladogram" && !use.edge.length) 2 else 1
if (node.pos == 1) {
yy <- .nodeHeight(z$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(z$edge[, 1]), as.integer(z$edge[, 2]),
as.integer(Nedge), double(Ntip + Nnode), as.double(yy))
xx <- ans[[5]] - 1
yy <- ans[[6]]
}
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$edge.length)
}
## TIDY
if (type == "tidy") {
if (!show.tip.label) {
yy <- tidy.xy(z$edge, Ntip, Nnode, xx, yy)
} else { # we add to xx the size taken by labels, so that tidying considers labels
xx.tips <- xx[1:Ntip]
pin1 <- par("pin")[1] # width of the device in inches
lab.strlength <- getStringLengthbyTip(xx.tips, x$tip.label, pin1, cex) #size of lab strings
xx2 <- xx
xx2[1:Ntip] <- xx2[1:Ntip] + lab.strlength
yy <- tidy.xy(z$edge, Ntip, Nnode, xx2, yy) #compress taking labels into account
}
}
### END TIDY
} else {
twopi <- 2 * pi
rotate.tree <- twopi * rotate.tree/360
if (type != "unrooted") { # for "fan" and "radial" trees (open.angle)
## 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))
}
switch(type, "fan" = {
theta <- .nodeHeight(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)
max_r <- max(r)
r <- (max_r - r + 1) / max_r
}
theta <- theta + rotate.tree
if (root.edge) r <- r + x$root.edge
xx <- r * cos(theta)
yy <- r * sin(theta)
}, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$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$M[, 2])
}, "radial" = {
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
r[r == 1] <- 0
r <- 1 - r/Ntip
theta <- .nodeHeight(z$edge, Nedge, theta) + rotate.tree
xx <- r * cos(theta)
yy <- r * sin(theta)
})
}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp - min(tmp) + 1
}
if (root.edge) {
if (direction == "rightwards") xx <- xx + x$root.edge
if (direction == "upwards") yy <- yy + x$root.edge
}
}
if (no.margin) par(mai = rep(0, 4))
if (show.tip.label) nchar.tip.label <- nchar(x$tip.label)
max.yy <- max(yy)
# if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
## REMOVED (2017-06-14)
xx.tips <- xx[1:Ntip]# * 1.04
if (show.tip.label) {
pin1 <- par("pin")[1] # width of the device in inches
tmp <- getLimit(xx.tips, x$tip.label, pin1, cex)
tmp <- tmp + label.offset
} else tmp <- max(xx.tips)
x_lim <- c(0, tmp)
if (direction == "leftwards") x_lim <- x_lim - (tmp - max(xx.tips))
} else {
### TIDY
## x.lim <- c(1, Ntip) # Not true anymore with tidy trees
x_lim <- c(1, max(xx[1:Ntip])) # add offset?
### END TIDY
}
} else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
x_lim <- range(xx) + c(-offset, offset)
} else x_lim <- range(xx)
}, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
x_lim <- c(0 - offset, max(xx) + offset)
} else x_lim <- c(0, max(xx))
}, "radial" = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.03 * cex)
x_lim <- c(-1 - offset, 1 + offset)
} else x_lim <- c(-1, 1)
})
# }
if (is.null(x.lim)){
x.lim <- x_lim
} else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal) x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
x.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy * cex)
if (type == "radial")
x.lim[1] <-
if (show.tip.label) -1 - max(nchar.tip.label * 0.03 * cex)
else -1
}
## mirror the xx:
if (phyloORclado && direction == "leftwards") xx <- x_lim[2] - xx
# if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal) {
### TIDY
## y.lim <- c(1, Ntip) # Not true anymore with tidy trees
y_lim <- c(1, max(yy[1:Ntip]))
### END TIDY
} else {
pin2 <- par("pin")[2] # height of the device in inches
## 1.04 comes from that we are using a regular axis system
## with 4% on both sides of the range of x:
## REMOVED (2017-06-14)
yy.tips <- yy[1:Ntip]# * 1.04
if (show.tip.label) {
tmp <- getLimit(yy.tips, x$tip.label, pin2, cex)
tmp <- tmp + label.offset
} else tmp <- max(yy.tips)
y_lim <- c(0, tmp)
if (direction == "downwards") y_lim <- y_lim - (tmp - max(yy.tips))
}
} else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar.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.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.tip.label * 0.03 * cex)
y_lim <- c(-1 - offset, 1 + offset)
} else y_lim <- c(-1, 1)
})
if (is.null(y.lim)) {
y.lim <- y_lim
} 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.tip.label * 0.018 * max.yy * cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label) -1 - max(nchar.tip.label * 0.018 * max.yy * cex) else -1
}
## mirror the yy:
if (phyloORclado && direction == "downwards") yy <- y_lim[2] - yy # fix by Klaus
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$tip.label, cex = cex))
loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
##xx <- xx + MAXSTRING
}
if (!horizontal) {
psr <- par("usr")
MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
##yy <- yy + MAXSTRING
srt <- 180 + srt
}
}
}
if (type %in% c("phylogram", "tidy")) {
phylogram.plot(x$edge, Ntip, Nnode, xx, yy, horizontal,
edge.color, edge.width, edge.lty,
node.color, node.width, node.lty)
} else {
if (is.null(edge.color)) {
edge.color <- par('fg')
}
if (is.null(edge.width)) {
edge.width <- par('lwd')
}
if (is.null(edge.lty)) {
edge.lty <- par('lty')
}
if (type == "fan") {
ereorder <- match(z$edge[, 2], x$edge[, 2])
if (length(edge.color) > 1) {
edge.color <- rep_len(edge.color, Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep_len(edge.width, Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep_len(edge.lty, 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) {
rootcol <- if (length(edge.color) == 1) edge.color else par("fg")
rootw <- if (length(edge.width) == 1) edge.width else par("lwd")
rootlty <- if (length(edge.lty) == 1) edge.lty else par("lty")
if (type == "fan") {
tmp <- polar2rect(x$root.edge, theta[ROOT])
segments(0, 0, tmp$x, tmp$y, col = rootcol, lwd = rootw, lty = rootlty)
} else {
switch(direction,
"rightwards" = segments(0, yy[ROOT], x$root.edge, yy[ROOT],
col = rootcol, lwd = rootw, lty = rootlty),
"leftwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT],
col = rootcol, lwd = rootw, lty = rootlty),
"upwards" = segments(xx[ROOT], 0, xx[ROOT], x$root.edge,
col = rootcol, lwd = rootw, lty = rootlty),
"downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge,
col = rootcol, lwd = rootw, lty = rootlty))
}
}
if (show.tip.label) {
if (is.expression(x$tip.label)) underscore <- TRUE
if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado) {
if (align.tip.label) {
xx.tmp <- switch(direction,
"rightwards" = max(xx[1:Ntip]),
"leftwards" = min(xx[1:Ntip]),
"upwards" = xx[1:Ntip],
"downwards" = xx[1:Ntip])
yy.tmp <- switch(direction,
"rightwards" = yy[1:Ntip],
"leftwards" = yy[1:Ntip],
"upwards" = max(yy[1:Ntip]),
"downwards" = min(yy[1:Ntip]))
segments(xx[1:Ntip], yy[1:Ntip], xx.tmp, yy.tmp, lty = align.tip.label.lty)
} else {
xx.tmp <- xx[1:Ntip]
yy.tmp <- yy[1:Ntip]
}
text(xx.tmp + lox, yy.tmp + loy, x$tip.label, adj = adj,
font = font, srt = srt, cex = cex, col = tip.color)
} else {
angle <- if (type == "unrooted") XY$axe else atan2(yy[1:Ntip], xx[1:Ntip]) # in radians
lab4ut <-
if (is.null(lab4ut)) {
if (type == "unrooted") "horizontal" else "axial"
} else match.arg(lab4ut, c("horizontal", "axial"))
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(angle) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] * 1.05
sel <- abs(angle) > pi/4 & abs(angle) < 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(angle)[sel] / pi - 0.5)
sel <- angle > pi / 4 & angle < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel] / 2
sel <- angle < -pi / 4 & angle > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
text(xx.tips + x.adj * cex, yy.tips + y.adj * cex,
x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
} else { # if lab4ut == "axial"
if (align.tip.label) {
POL <- rect2polar(xx.tips, yy.tips)
POL$r[] <- max(POL$r)
REC <- polar2rect(POL$r, POL$angle)
xx.tips <- REC$x
yy.tips <- REC$y
segments(xx[1:Ntip], yy[1:Ntip], xx.tips, yy.tips, lty = align.tip.label.lty)
}
if (type == "unrooted") {
adj <- abs(angle) > pi/2
angle <- angle * 180/pi # switch to degrees
angle[adj] <- angle[adj] - 180
adj <- as.numeric(adj)
} else {
s <- xx.tips < 0
angle <- angle * 180/pi
angle[s] <- angle[s] + 180
adj <- as.numeric(s)
}
## `srt' takes only a single value, so can't vectorize this:
## (and need to 'elongate' these vectors:)
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip)
text(xx.tips[i], yy.tips[i], x$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$node.label, adj = adj, font = font, srt = srt, cex = cex)
}
L <- list(type = type, use.edge.length = use.edge.length,
node.pos = node.pos, node.depth = node.depth,
show.tip.label = show.tip.label,
show.node.label = show.node.label, font = font,
cex = cex, adj = adj, srt = srt, no.margin = no.margin,
label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
direction = direction, tip.color = tip.color,
Ntip = Ntip, Nnode = Nnode, root.time = x$root.time,
align.tip.label = align.tip.label)
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 = NULL, edge.width = NULL,
edge.lty = NULL,
node.color = NULL, node.width = NULL,
node.lty = NULL)
{
nodes <- Ntip + seq_len(Nnode)
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp
}
## un trait vertical a chaque noeud...
x0v <- xx[nodes]
y0v <- y1v <- numeric(Nnode)
e1 <- edge[, 1]
e2 <- edge[, 2]
Nedge <- length(e1)
## store the index of each node in the 1st column of edge:
NodeInEdge1 <- lapply(Ntip + seq_len(Nnode), function (j) which(e1 == j))
edgeChildren <- lapply(NodeInEdge1, function (nie) e2[nie])
yv <- vapply(edgeChildren, function (i) range(yy[i]), double(2))
y0v <- yv[1, ]
y1v <- yv[2, ]
## ... et un trait horizontal partant de chaque tip et chaque noeud
## vers la racine
x0h <- xx[e1]
x1h <- xx[e2]
y0h <- yy[e2]
# Node and edge styling
.one.style <- function (style) {
list(h = rep_len(style, Nedge), v = rep_len(style, Ntip + Nnode))
}
.edge.style <- function (node.style) {
node.style <- rep_len(node.style, Ntip + Nnode)
sapply(seq_len(Nedge), function (e) node.style[e2[e]])
}
.node.style <- function (edge.style, fallback) {
edge.style <- rep_len(edge.style, Nedge)
c(character(Ntip),
sapply(Ntip + seq_len(Nnode), function (n) {
pendant.styles <- edge.style[e1 == n]
if (length(unique(pendant.styles)) == 1L) {
pendant.styles[1]
} else {
fallback
}
}))
}
.style <- function (edge.style, node.style, stylePar) {
if (missing(edge.style) || is.null(edge.style)) {
if (missing(node.style) || is.null(node.style)) {
return(.one.style(par(stylePar)))
} else {
if (length(node.style) == 1L) {
return(.one.style(node.style))
} else {
return(list(h = .edge.style(node.style),
v = rep_len(node.style, Ntip + Nnode)))
}
}
} else if (missing(node.style) || is.null(node.style)) {
if (length(edge.style) == 1L) {
return(.one.style(edge.style))
} else {
return(list(h = rep_len(edge.style, Nedge),
v = .node.style(edge.style, par(stylePar))))
}
} else {
return(list(h = rep_len(edge.style, Nedge),
v = rep_len(node.style, Ntip + Nnode)))
}
}
.LtyToStr <- function (x) {
if (is.numeric(x)) {
c("blank", "solid", "dashed", "dotted", "dotdash", "longdash",
"twodash")[x + 1L]
} else {
x
}
}
colors <- .style(edge.color, node.color, 'fg')
widths <- .style(edge.width, node.width, 'lwd')
ltys <- .style(.LtyToStr(edge.lty), .LtyToStr(node.lty), 'lty')
edge.color <- colors$h
edge.width <- widths$h
edge.lty <- ltys$h
color.v <- colors$v[-seq_len(Ntip)]
width.v <- widths$v[-seq_len(Ntip)]
lty.v <- ltys$v[-seq_len(Ntip)]
DF <- data.frame(edge.color, edge.width, edge.lty, stringsAsFactors = FALSE)
DF <- DF[, c(is.null(node.color), is.null(node.width), is.null(node.lty)),
drop = FALSE]
for (i in seq_len(Nnode)) {
br <- NodeInEdge1[[i]]
if (length(br) == 2) {
A <- br[1]
B <- br[2]
# We should draw a single line if at all possible, for the
# appearance of dotted / dashed line styles.
if (any(DF[A, ] != DF[B, ])) {
## add a new line:
y0v <- c(y0v, y0v[i])
y1v <- c(y1v, yy[i + Ntip])
x0v <- c(x0v, x0v[i])
## shorten the old line:
y0v[i] <- yy[i + Ntip]
if (is.null(node.color)) {
# Half-lines may have different colours
color.v[i] <- edge.color[B]
color.v <- c(color.v, edge.color[A])
} else {
# Use node colour for both half-lines
color.v <- c(color.v, color.v[i])
}
if (is.null(node.width)) {
width.v[i] <- edge.width[B]
width.v <- c(width.v, edge.width[A])
} else {
width.v <- c(width.v, width.v[i])
}
if (is.null(node.lty)) {
lty.v[i] <- edge.lty[B]
lty.v <- c(lty.v, edge.lty[A])
} else {
lty.v <- c(lty.v, lty.v[i])
}
}
}
}
if (horizontal) {
# draw horizontal lines
segments(x0h, y0h, x1h, y0h,
col = edge.color, lwd = edge.width, lty = edge.lty)
# draw vertical lines
segments(x0v, y0v, x0v, y1v,
col = color.v, lwd = width.v, lty = lty.v)
} else {
# draws vertical lines
segments(y0h, x0h, y0h, x1h,
col = edge.color, lwd = edge.width, lty = edge.lty)
# draws horizontal lines
segments(y0v, x0v, y1v, x0v,
col = color.v, lwd = width.v, lty = lty.v)
}
}
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(as.list(rep(edge.feat, Nnode)))
edge.feat <- rep(edge.feat, length.out = Nedge)
feat.arc <- as.list(rep(default, Nnode))
for (k in 1:Nnode) {
tmp <- edge.feat[start[k]]
if (tmp == edge.feat[end[k]]) { # fix by Francois Michonneau (2015-07-24)
feat.arc[[k]] <- tmp
} else {
if (nodedegree[k] == 2)
feat.arc[[k]] <- rep(c(tmp, edge.feat[end[k]]), each = 50)
}
}
feat.arc
}
nodedegree <- tabulate(edge[, 1L])[-seq_len(Ntip)]
co <- foo(edge.color, par("fg"))
lw <- foo(edge.width, par("lwd"))
ly <- foo(edge.lty, par("lty"))
for (k in 1:Nnode) {
i <- start[k]
j <- end[k]
# make number of segments dependent on the angle
n_segments <- abs(as.integer(2 + abs(theta[edge[j, 2]] - theta[edge[i, 2]]) / 0.03))
X <- rep(r[edge[i, 1]], n_segments)
Y <- seq(theta[edge[i, 2]], theta[edge[j, 2]], length.out = n_segments)
x <- X * cos(Y); y <- X * sin(Y)
x0 <- x[-n_segments]; y0 <- y[-n_segments]; x1 <- x[-1]; y1 <- y[-1]
segments(x0, y0, x1, y1, 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
## make sure that the 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$edge)[1]
phy <- reorder(phy, order = "postorder")
.C(node_depth, as.integer(n),
as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
as.integer(N), double(n + m), as.integer(method))[[5]]
}
node.depth.edgelength <- function(phy)
{
n <- length(phy$tip.label)
m <- phy$Nnode
N <- dim(phy$edge)[1]
phy <- reorder(phy, order = "postorder")
.C(node_depth_edgelength, as.integer(phy$edge[, 1]),
as.integer(phy$edge[, 2]), as.integer(N),
as.double(phy$edge.length), double(n + m))[[5]]
}
node.height <- function(phy, clado.style = FALSE)
{
n <- length(phy$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$edge[, 2]
if (clado.style)
.C(node_height_clado, as.integer(n), as.integer(e1),
as.integer(e2), as.integer(N), double(n + m), as.double(yy))[[6]]
else
.C(node_height, as.integer(e1), as.integer(e2), as.integer(N),
as.double(yy))[[4]]
}
plot.multiPhylo <- function(x, layout = 1, ...)
{
layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
if (!devAskNewPage() && names(dev.cur()) %in% deviceIsInteractive()) {
devAskNewPage(TRUE)
on.exit(devAskNewPage(FALSE))
}
for (i in seq_along(x)) plot(x[[i]], ...)
}
trex <- function(phy, title = TRUE, subbg = "lightyellow3",
return.tree = FALSE, ...)
{
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
devmain <- dev.cur() # where the main tree is plotted
restore <- function() {
dev.set(devmain)
assign("last_plot.phylo", lastPP, envir = .PlotPhyloEnv)
}
on.exit(restore())
NEW <- TRUE
cat("Click close to a node. Right-click to exit.\n")
repeat {
x <- identify.phylo(phy, quiet = TRUE)
if (is.null(x)) return(invisible(NULL)) else {
x <- x$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, ...,
direction = ifelse(horiz, "rightwards", "upwards"), side=2)
{
op <- par(no.readonly = TRUE)
on.exit({
par(op)
devAskNewPage(FALSE)
})
par(mar = rep(0.5, 4), oma = rep(2, 4))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
horiz <- ifelse(direction %in% c("rightwards", "leftwards"), TRUE, FALSE)
rts <- sapply(x, function(x) branching.times(x)[1])
maxrts <- max(rts)
lim <- cbind(rts - maxrts, rts)
if (direction %in% c("leftwards", "downwards")) {
lim[,1] <- 0
lim[,2] <- maxrts
}
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)
}
if (horiz) {
for (i in 1:Ntree){
plot(x[[i]], x.lim = lim[i, ], direction = direction, ...)
if(i == 1 && 1 %in% side) axisPhylo(side=3)
}
} else {
for (i in 1:Ntree){
plot(x[[i]], y.lim = lim[i, ], direction = direction, ...)
if(i == 1 && 1 %in% side) axisPhylo(side=2)
}
}
if (2 %in% side) axisPhylo(if (horiz) 1 else 4)
invisible(x)
}
tidy.xy <- function(edge, Ntip, Nnode, xx, yy)
{
yynew <- yy # will be updated to get the new y coordinates after tidying
## initialrange<-diff(range(yy)) #for computing compression. Remove ?
oedge <- edge[match(seq_len(Ntip + Nnode), edge[, 2]), 1] # ordered edges
segofnodes <- data.frame(x1 = xx[oedge], y1 = yy, x2 = xx, y2 = yy) # segment associated to each node
postordernodes <- edge[,2]
nodes <- c(postordernodes[order(xx[postordernodes], decreasing = TRUE)], Ntip + 1) # ensures equal x values to not lead to erroneuos postoder of nodes
GetContourPairsFromSegments <- function(seg, which) {
if (nrow(seg) > 1) { #solves issue with branch length = 0
allx <- sort(unique(c(seg$x1, seg$x2)))
newx2 <- allx[2:length(allx)]
if (which == "top") {
newy2i <- sapply(newx2, function(cx, se) which(cx > se$x1 & cx <= se$x2)[which.max(se$y1[which(cx > se$x1 & cx <= se$x2)])], se = seg)
}
if (which == "bottom") {
newy2i <- sapply(newx2, function(cx, se) which(cx > se$x1 & cx <= se$x2)[which.min(se$y1[which(cx > se$x1 & cx <= se$x2)])], se = seg)
}
newx1 <- allx[1:(length(allx) - 1)]
newy1i <- newy2i
## we simplify segments by merging thsoe on same horiz (bout a bout)
where2mergei <- which((newy1i[2:length(newy1i)] - newy2i[1:(length(newy1i) - 1)]) == 0)
if (length(where2mergei) > 0) {
newx1 <- newx1[-(where2mergei + 1)]
newy1i <- newy1i[-(where2mergei + 1)]
newx2 <- newx2[-(where2mergei)]
newy2i <- newy2i[-(where2mergei)]
}
newy1ok <- seg$y1[newy1i]
newy2ok <- newy1ok
newseg <- data.frame(x1 = newx1, y1 = newy1ok, x2 = newx2, y2 = newy2ok)
} else {
newseg <- seg
}
newseg
}
GetMinDistBetweenContours <- function(topcontour, bottomcontour) {
## efficient way to compare top and bottom contour by only looking
## at necessary pairs (see original publiction)
d <- NULL
topi <- 1
boti <- 1
while((topi <= nrow(topcontour)) & (boti <= nrow(bottomcontour))) {
d <- c(d, bottomcontour[boti, ]$y1 - topcontour[topi, ]$y1)
if (bottomcontour[boti, ]$x2 < topcontour[topi, ]$x2) boti <- boti + 1
else topi <- topi + 1
}
min(d)
}
N <- list() # will contain all info for each node.
for (n in nodes) {
N[[n]] <- list()
childs <- edge[edge[, 1] == n, 2]
childs.ord <- childs[order(yy[childs])] # childs ordered by y values
desc <- c(childs, unlist(lapply(N[childs], function(x) x$desc)))
diffiny <- 0
if (n > Ntip) { # we are in a node
oldyofcurrentnode <- yynew[n]
for (nn in 2:length(childs.ord)) {
top <- N[[childs.ord[nn - 1]]]$segtop
bot <- N[[childs.ord[nn]]]$segbottom
mindist <- GetMinDistBetweenContours(top, bot)
if (mindist != 1) { # There is room for tidying or untidy up if branches are tangled
mod <- mindist - 1
N[[childs.ord[nn]]]$segbottom[, c(2, 4)] <- N[[childs.ord[nn]]]$segbottom[, c(2, 4)] - mod
N[[childs.ord[nn]]]$segtop[, c(2, 4)] <- N[[childs.ord[nn]]]$segtop[, c(2, 4)] - mod
yynew[c(childs.ord[nn], N[[childs.ord[nn]]]$desc)] <- yynew[c(childs.ord[nn], N[[childs.ord[nn]]]$desc)] - mod
}
}
newyofcurrentnode <- mean(range(yynew[childs.ord]))
yynew[n] <- newyofcurrentnode
diffiny <- oldyofcurrentnode - newyofcurrentnode
}
descseg <- segofnodes[n, ]
descseg[, c(2, 4)] <- descseg[, c(2, 4)] - diffiny
segtop.pre <- rbind(descseg, do.call(rbind, lapply(N[childs], function(x) x$segtop)))
segtop <- GetContourPairsFromSegments(segtop.pre, "top")
segbottom.pre <- rbind(descseg, do.call(rbind, lapply(N[childs], function(x) x$segbottom)))
segbottom <- GetContourPairsFromSegments(segbottom.pre, "bottom")
N[[n]]$childs <- childs.ord
N[[n]]$desc <- desc
N[[n]]$segtop <- segtop
N[[n]]$segbottom <- segbottom
}
yynew <- yynew - (min(yynew) - 1) ## so that min(y)=1 always
## finalrange <- diff(range(yynew)) #for computing compression. Remove?
## compression <- ((initialrange-finalrange)/initialrange)*100 # Remove?
## print(paste("Compression: ", round(compression,2),"%", sep="")) #Remove?
yynew
}
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