-## plot.phylo.R (2010-01-04)
+## plot.phylo.R (2013-01-11)
## Plot Phylogenies
-## Copyright 2002-2010 Emmanuel Paradis
+## 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.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$tip.label)
- if (Ntip == 1) {
- warning("found only one tip in the tree")
+ if (Ntip < 2) {
+ warning("found less than 2 tips in the tree")
return(NULL)
}
if (any(tabulate(x$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 {
+ 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, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
+ 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))
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
r <- 1/r
}
- xx <- r*cos(theta)
- yy <- r*sin(theta)
+ theta <- theta + rotate.tree
+ xx <- r * cos(theta)
+ yy <- r * sin(theta)
}, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$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])
## radius:
X <- 1 - X/Ntip
## angle (1st compute the angles for the tips):
- yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
+ yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode))
Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
- xx <- X * cos(Y)
- yy <- X * sin(Y)
- })
+ xx <- X * cos(Y + rotate.tree)
+ yy <- X * sin(Y + rotate.tree)
+ })}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
}
x.lim[2] <- tmp
- if (direction == "leftwards") xx <- x.lim[2] - xx #max(xx[ROOT] + tmp)
-# else max(xx[1:Ntip] + tmp)
} else x.lim <- c(1, Ntip)
} else switch(type, "fan" = {
if (show.tip.label) {
if (show.tip.label) -1 - max(nchar(x$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 {
tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
}
y.lim[2] <- tmp
- if (direction == "downwards") yy <- y.lim[2] - yy
}
} else switch(type, "fan" = {
if (show.tip.label) {
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")) 1 else NA # fix by Klaus Schliep (2008-03-28)
+ 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")
"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$tip.label)
if (phyloORclado)
y.adj[sel] <- strheight(x$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
+ 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.tips <- xx[1:Ntip]
- ## using atan2 considerably facilitates things compared to acos...
- angle <- atan2(yy[1:Ntip], xx.tips)*180/pi
+ 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 <- numeric(Ntip)
- adj[xx.tips < 0] <- 1
+ 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,
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:
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)
+ 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)
}
}
-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)
- layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
- else layout(matrix(1))
- if (!par("ask")) {
- par(ask = TRUE)
- on.exit(par(ask = FALSE))
+ 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 ;)
+}
projects / ape.git / blobdiff