-## plot.phylo.R (2008-02-08)
+## plot.phylo.R (2012-12-19)
## Plot Phylogenies
-## Copyright 2002-2008 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, 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,
+ open.angle = 0, ...)
{
Ntip <- length(x$tip.label)
- if (Ntip == 1) stop("found only one tip in the tree!")
- Nedge <- dim(x$edge)[1]
+ if (Ntip < 2) {
+ warning("found less than 2 tips in the tree")
+ return(NULL)
+ }
if (any(tabulate(x$edge[, 1]) == 1))
- stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles().")
+ stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
+
+ .nodeHeight <- function(Ntip, Nnode, edge, Nedge, yy)
+ .C("node_height", as.integer(Ntip), as.integer(Nnode),
+ as.integer(edge[, 1]), as.integer(edge[, 2]),
+ as.integer(Nedge), as.double(yy),
+ DUP = FALSE, PACKAGE = "ape")[[6]]
+
+ .nodeDepth <- function(Ntip, Nnode, edge, Nedge)
+ .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+ as.integer(edge[, 1]), as.integer(edge[, 2]),
+ as.integer(Nedge), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[6]]
+
+ .nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
+ .C("node_depth_edgelength", as.integer(Ntip),
+ as.integer(Nnode), as.integer(edge[, 1]),
+ as.integer(edge[, 2]), as.integer(Nedge),
+ as.double(edge.length), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[7]]
+
+ Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length)) use.edge.length <- FALSE
- if (type == "unrooted" || !use.edge.length) root.edge <- 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$edge # to save
if (phyloORclado) {
## we first compute the y-coordinates of the tips.
- ## Fix from Klaus Schliep (2007-06-16):
- if (!is.null(attr(x, "order")))
- if (attr(x, "order") == "pruningwise")
- x <- reorder(x)
- ## End of fix
+ phyOrder <- attr(x, "order")
+ ## make sure the tree is in cladewise order:
+ if (is.null(phyOrder) || phyOrder != "cladewise") {
+ x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
+ if (!identical(x$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$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
- edge.color <- rep(edge.color, length.out = Nedge)
- edge.width <- rep(edge.width, length.out = Nedge)
- ## fix from Li-San Wang (2007-01-23):
- xe <- x$edge
- x <- reorder(x, order = "pruningwise")
- ereorder <- match(x$edge[, 2], xe[, 2])
- edge.color <- edge.color[ereorder]
- edge.width <- edge.width[ereorder]
- ## End of fix
+ ## 'z' is the tree in pruningwise order used in calls to .C
+ z <- reorder(x, order = "pruningwise")
+
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
if (type == "cladogram" && !use.edge.length) node.pos <- 2
}
if (node.pos == 1)
- yy <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), as.double(yy),
- DUP = FALSE, PACKAGE = "ape")[[6]]
+ yy <- .nodeHeight(Ntip, Nnode, z$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(x$edge[, 1]),
- as.integer(x$edge[, 2]), as.integer(Nedge),
+ as.integer(Nnode), as.integer(z$edge[, 1]),
+ as.integer(z$edge[, 2]), as.integer(Nedge),
double(Ntip + Nnode), as.double(yy),
DUP = FALSE, PACKAGE = "ape")
xx <- ans[[6]] - 1
yy <- ans[[7]]
}
if (!use.edge.length) {
- if(node.pos != 2)
- xx <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[6]] - 1
+ if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) - 1
xx <- max(xx) - xx
} else {
- xx <- .C("node_depth_edgelength", as.integer(Ntip),
- as.integer(Nnode), as.integer(x$edge[, 1]),
- as.integer(x$edge[, 2]), as.integer(Nedge),
- as.double(x$edge.length), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[7]]
+ xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
- }
- if (type == "fan") {
+ } 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 <- xe[which(xe[, 2] <= Ntip), 2]
- xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
+ 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 <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), theta, DUP = FALSE,
- PACKAGE = "ape")[[6]]
+ theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
if (use.edge.length) {
- r <- .C("node_depth_edgelength", as.integer(Ntip),
- as.integer(Nnode), as.integer(x$edge[, 1]),
- as.integer(x$edge[, 2]), as.integer(Nedge),
- as.double(x$edge.length), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[7]]
+ r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
} else {
- r <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[6]]
+ r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
r <- 1/r
}
- xx <- r*cos(theta)
- yy <- r*sin(theta)
-
- }
- if (type == "unrooted") {
+ theta <- theta + rotate.tree
+ xx <- r * cos(theta)
+ yy <- r * sin(theta)
+ }, "unrooted" = {
+ nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length)
- unrooted.xy(Ntip, Nnode, x$edge, x$edge.length)
+ unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree)
else
- unrooted.xy(Ntip, Nnode, x$edge, rep(1, Nedge))
+ unrooted.xy(Ntip, Nnode, z$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])
- }
- if (type == "radial") {
- X <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[6]]
+ }, "radial" = {
+ X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
X[X == 1] <- 0
## radius:
X <- 1 - X/Ntip
## angle (1st compute the angles for the tips):
- yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
- Y <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
- as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
- as.integer(Nedge), as.double(yy),
- DUP = FALSE, PACKAGE = "ape")[[6]]
- xx <- X * cos(Y)
- yy <- X * sin(Y)
- }
- if (phyloORclado && direction != "rightwards") {
- if (direction == "leftwards") {
- xx <- -xx
- xx <- xx - min(xx)
- }
+ yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode))
+ Y <- .nodeHeight(Ntip, Nnode, z$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 (direction == "downwards") {
- yy <- -yy
- yy <- yy - min(yy)
- }
}
- }
- if (phyloORclado && root.edge) {
- if (direction == "rightwards") xx <- xx + x$root.edge
- if (direction == "upwards") yy <- yy + x$root.edge
+ 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)
- tmp <-
- if (show.tip.label) nchar(x$tip.label) * 0.018 * max(xx) * cex
- else 0
- x.lim[2] <-
- if (direction == "leftwards") max(xx[ROOT] + tmp)
- else max(xx[1:Ntip] + tmp)
+ pin1 <- par("pin")[1] # width of the device in inches
+ strWi <- strwidth(x$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))$root, silent = TRUE)
+ ## if the above fails, give 1/3 of the device for the tip labels:
+ if (is.character(alp)) tmp <- max(xx.tips)*1.5 else {
+ tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
+ }
+ x.lim[2] <- tmp
} else x.lim <- c(1, Ntip)
- }
- if (type == "fan") {
+ } else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(min(xx) - offset, max(xx) + offset)
} else x.lim <- c(min(xx), max(xx))
- }
- if (type == "unrooted") {
+ }, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
- }
- if (type == "radial") {
+ }, "radial" = {
if (show.tip.label) {
offset <- max(nchar(x$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 (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
else -1
}
+ ## mirror the xx:
+ if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal) y.lim <- c(1, Ntip) else {
y.lim <- c(0, NA)
- tmp <-
- if (show.tip.label) nchar(x$tip.label) * 0.018 * max(yy) * cex
- else 0
- y.lim[2] <-
- if (direction == "downwards") max(yy[ROOT] + tmp)
- else max(yy[1:Ntip] + tmp)
+ 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
}
- }
- if (type == "fan") {
+ } else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
- }
- if (type == "unrooted") {
+ }, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
- }
- if (type == "radial") {
+ }, "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)
+ 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$tip.label) * 0.018 * max(yy) * cex) else -1
}
+ ## mirror the yy:
+ if (phyloORclado && direction == "downwards") yy <- max(yy) - yy
if (phyloORclado && root.edge) {
if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
}
+ asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
+ plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
- plot(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
- ylab = "", xaxt = "n", yaxt = "n", bty = "n", ...)
+if (plot) {
if (is.null(adj))
- adj <- if (phyloORclado && direction == "leftwards") 1 else 0
- if (phyloORclado) {
+ adj <- if (phyloORclado && direction == "leftwards") 1 else 0
+ if (phyloORclado && show.tip.label) {
MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
+ loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
- loy <- 0
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
- loy <- 0
- xx <- xx + MAXSTRING
+ ##xx <- xx + MAXSTRING
}
if (!horizontal) {
psr <- par("usr")
- MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3]) / (psr[2] - psr[1])
+ 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
+ ##yy <- yy + MAXSTRING
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
- horizontal, edge.color, edge.width)
+ horizontal, edge.color, edge.width, edge.lty)
} else {
- if (type == "fan")
- circular.plot(x$edge, Ntip, Nnode, xx, yy, theta,
- r, edge.color, edge.width)
- else
- cladogram.plot(x$edge, xx, yy, edge.color, edge.width)
+ if (type == "fan") {
+ ereorder <- match(z$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$edge, xx, yy, edge.color, edge.width, edge.lty)
}
if (root.edge)
switch(direction,
"upwards" = segments(xx[ROOT], 0, xx[ROOT], x$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) {
+
+ if (phyloORclado)
text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label, adj = adj,
font = font, srt = srt, cex = cex, col = tip.color)
- }
+
if (type == "unrooted") {
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
y.adj[sel] <- strheight(x$tip.label)[sel] / 2
sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
- text(xx[1:Ntip] + x.adj*cex, yy[1:Ntip] + y.adj*cex,
+ text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex,
x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
} else { # if lab4ut == "axial"
- adj <- as.numeric(abs(XY$axe) > pi/2)
- srt <- 180*XY$axe/pi
- srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
- ## <FIXME> temporary check of the values of `srt':
- ## set to 0 if "-0.000001 < srt < 0"
- sel <- srt > -1e-6 & srt < 0
- if (any(sel)) srt[sel] <- 0
- ## </FIXME>
- ## `srt' takes only a single value, so we cannot vectorize this:
+ 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[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
- font = font, srt = srt[i], col = tip.color[i])
+ text(xx.tips[i], yy.tips[i], cex = cex[i],
+ x$tip.label[i], adj = adj[i], font = font[i],
+ srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
- xx.scaled <- xx[1:Ntip]
- if (type == "fan") { # no need if type == "radial"
- maxx <- max(xx.scaled)
- if (maxx > 1) xx.scaled <- xx.scaled/maxx
+ 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)
}
- angle <- acos(xx.scaled)*180/pi
- s1 <- angle > 90 & yy[1:Ntip] > 0
- s2 <- angle < 90 & yy[1:Ntip] < 0
- s3 <- angle > 90 & yy[1:Ntip] < 0
- angle[s1] <- angle[s1] + 180
- angle[s2] <- -angle[s2]
- angle[s3] <- 180 - angle[s3]
- adj <- numeric(Ntip)
- adj[xx[1:Ntip] < 0] <- 1
- ## `srt' takes only a single value, so we cannot vectorize this:
+ 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[i], yy[i], x$tip.label[i], font = font, cex = cex,
- srt = angle[i], adj = adj[i], col = tip.color[i])
+ text(xx.tips[i], yy.tips[i], x$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$node.label, adj = adj, font = font, srt = srt, cex = cex)
+ text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
+ x$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,
label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
direction = direction, tip.color = tip.color,
Ntip = Ntip, Nnode = Nnode)
- assing("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
+ 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)
+phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
+ edge.color, edge.width, edge.lty)
{
nodes <- (Ntip + 1):(Ntip + Nnode)
if (!horizontal) {
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:
+ NodeInEdge1 <- vector("list", Nnode)
for (i in nodes) {
- j <- edge[which(edge[, 1] == i), 2]
- y0v[i - Ntip] <- min(yy[j])
- y1v[i - Ntip] <- max(yy[j])
+ 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
- sq <- if (Nnode == 1) 1:Ntip else c(1:Ntip, nodes[-1])
- y0h <- yy[sq]
- x1h <- xx[sq]
- ## match() is very useful here becoz each element in edge[, 2] is
- ## unique (not sure this is so useful in edge[, 1]; needs to be checked)
- ## `pos' gives for each element in `sq' its index in edge[, 2]
- pos <- match(sq, edge[, 2])
- x0h <- xx[edge[pos, 1]]
-
- e.w <- unique(edge.width)
- if (length(e.w) == 1) width.v <- rep(e.w, Nnode)
- else {
- width.v <- rep(1, Nnode)
- for (i in 1:Nnode) {
- br <- edge[which(edge[, 1] == i + Ntip), 2]
- width <- unique(edge.width[br])
- if (length(width) == 1) width.v[i] <- width
- }
- }
- e.c <- unique(edge.color)
- if (length(e.c) == 1) color.v <- rep(e.c, Nnode)
- else {
+ 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 <- which(edge[, 1] == i + Ntip)
- #br <- edge[which(edge[, 1] == i + Ntip), 2]
- color <- unique(edge.color[br])
- if (length(color) == 1) color.v[i] <- color
+ 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]
+ }
+ }
}
}
- ## we need to reorder `edge.color' and `edge.width':
- edge.width <- edge.width[pos]
- edge.color <- edge.color[pos]
if (horizontal) {
- segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v) # draws vertical lines
- segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width) # draws horizontal lines
+ 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(y0v, x0v, y1v, x0v, col = color.v, lwd = width.v) # draws horizontal lines
- segments(y0h, x0h, y0h, x1h, col = edge.color, lwd = edge.width) # draws vertical lines
+ 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)
- segments(xx[edge[, 1]], yy[edge[, 1]], xx[edge[, 2]], yy[edge[, 2]],
- col = edge.color, lwd = edge.width)
+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)
+ r, edge.color, edge.width, edge.lty)
+### 'edge' must be in pruningwise order
{
r0 <- r[edge[, 1]]
r1 <- r[edge[, 2]]
theta0 <- theta[edge[, 2]]
+ costheta0 <- cos(theta0)
+ sintheta0 <- sin(theta0)
- x0 <- r0*cos(theta0)
- y0 <- r0*sin(theta0)
- x1 <- r1*cos(theta0)
- y1 <- r1*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)
+ 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)
- end <- c(tmp, dim(edge)[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)
- co <- if (edge.color[i] == edge.color[j]) edge.color[i] else "black"
- lw <- if (edge.width[i] == edge.width[j]) edge.width[i] else 1
- lines(X*cos(Y), X*sin(Y), col = co, lwd = lw)
+ lines(X*cos(Y), X*sin(Y), col = co[k], lwd = lw[k], lty = ly[k])
}
}
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length)
+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])
}
- root <- Ntip + 1
Nedge <- dim(edge)[1]
yy <- xx <- numeric(Ntip + Nnode)
- nb.sp <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
- as.integer(edge[, 1]), as.integer(edge[, 2]),
- as.integer(Nedge), double(Ntip + Nnode),
- DUP = FALSE, PACKAGE = "ape")[[6]]
## `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...
- ## xx[root] <- yy[root] <- 0 # already set!
- foo(root, 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)
par(ask = TRUE)
on.exit(par(ask = FALSE))
}
- for (i in x) plot(i, ...)
+ 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 && !par("ask")) {
+ par(ask = TRUE)
+ on.exit(par(ask = 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 ;)
}
projects / ape.git / blobdiff