-## plot.phylo.R (2010-08-12)
+## plot.phylo.R (2008-05-08)
## Plot Phylogenies
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2008 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"),
+ 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", ...)
{
Ntip <- length(x$tip.label)
- if (Ntip == 1) {
- warning("found only one tip in the tree")
- return(NULL)
- }
- if (any(tabulate(x$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, 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]]
-
+ if (Ntip == 1) stop("found only one tip in the tree!")
Nedge <- dim(x$edge)[1]
+ if (any(tabulate(x$edge[, 1]) == 1))
+ stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles().")
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
-
- ## 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
- }
-
+ if (type == "unrooted" || !use.edge.length) 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$edge[, 2], xe[, 2])
- if (length(edge.color) > 1) {
- edge.color <- rep(edge.color, length.out = Nedge)
- edge.color <- edge.color[ereorder]
- }
- if (length(edge.width) > 1) {
- edge.width <- rep(edge.width, length.out = Nedge)
- edge.width <- edge.width[ereorder]
- }
- if (length(edge.lty) > 1) {
- edge.lty <- rep(edge.lty, length.out = Nedge)
- edge.lty <- edge.lty[ereorder]
- }
- }
- }
-### By contrats to ape (< 2.4), the arguments edge.color, etc., are
-### not elongated before being passed to segments(), except if needed
-### to be reordered
+ ## Fix from Klaus Schliep (2007-06-16):
+ if (!is.null(attr(x, "order")))
+ if (attr(x, "order") == "pruningwise")
+ x <- reorder(x)
+ ## End of fix
yy <- numeric(Ntip + Nnode)
TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
- ## 'z' is the tree in pruningwise order used in calls to .C
- z <- reorder(x, order = "pruningwise")
-### edge.color <- rep(edge.color, length.out = Nedge)
-### edge.width <- rep(edge.width, length.out = Nedge)
-### edge.lty <- rep(edge.lty, length.out = Nedge)
-### ## fix from Li-San Wang (2007-01-23):
-### xe <- x$edge
-### x <- reorder(x, order = "pruningwise")
-### ereorder <- match(x$edge[, 2], xe[, 2])
-### edge.color <- edge.color[ereorder]
-### edge.width <- edge.width[ereorder]
-### edge.lty <- edge.lty[ereorder]
-### ## end of fix
+ edge.color <- rep(edge.color, length.out = Nedge)
+ edge.width <- rep(edge.width, length.out = Nedge)
+ ## fix from Li-San Wang (2007-01-23):
+ xe <- x$edge
+ x <- reorder(x, order = "pruningwise")
+ ereorder <- match(x$edge[, 2], xe[, 2])
+ edge.color <- edge.color[ereorder]
+ edge.width <- edge.width[ereorder]
+ ## End of fix
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
if (type == "cladogram" && !use.edge.length) node.pos <- 2
}
if (node.pos == 1)
- yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
+ 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]]
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),
+ as.integer(Nnode), as.integer(x$edge[, 1]),
+ as.integer(x$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 <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) - 1
+ if(node.pos != 2)
+ xx <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+ as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+ as.integer(Nedge), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[6]] - 1
xx <- max(xx) - xx
} else {
- xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
+ xx <- .C("node_depth_edgelength", as.integer(Ntip),
+ as.integer(Nnode), as.integer(x$edge[, 1]),
+ as.integer(x$edge[, 2]), as.integer(Nedge),
+ as.double(x$edge.length), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[7]]
}
- } else switch(type, "fan" = {
+ }
+ if (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]
+ TIPS <- xe[which(xe[, 2] <= Ntip), 2]
xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
- theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
+ theta <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
+ as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+ as.integer(Nedge), theta, DUP = FALSE,
+ PACKAGE = "ape")[[6]]
if (use.edge.length) {
- r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
+ r <- .C("node_depth_edgelength", as.integer(Ntip),
+ as.integer(Nnode), as.integer(x$edge[, 1]),
+ as.integer(x$edge[, 2]), as.integer(Nedge),
+ as.double(x$edge.length), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[7]]
} else {
- r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
+ r <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+ as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+ as.integer(Nedge), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[6]]
r <- 1/r
}
xx <- r*cos(theta)
yy <- r*sin(theta)
- }, "unrooted" = {
- nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
+
+ }
+ if (type == "unrooted") {
XY <- if (use.edge.length)
- unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp)
+ unrooted.xy(Ntip, Nnode, x$edge, x$edge.length)
else
- unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp)
+ unrooted.xy(Ntip, Nnode, x$edge, rep(1, Nedge))
## 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$edge, Nedge)
+ }
+ if (type == "radial") {
+ X <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+ as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+ as.integer(Nedge), double(Ntip + Nnode),
+ DUP = FALSE, PACKAGE = "ape")[[6]]
X[X == 1] <- 0
## radius:
X <- 1 - X/Ntip
## angle (1st compute the angles for the tips):
yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
- Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
+ 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) {
+ }
+ if (phyloORclado && direction != "rightwards") {
+ if (direction == "leftwards") {
+ xx <- -xx
+ xx <- xx - min(xx)
+ }
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 (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 (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
+ tmp <-
+ if (show.tip.label) nchar(x$tip.label) * 0.018 * max(xx) * cex
+ else 0
+ x.lim[2] <-
+ if (direction == "leftwards") max(xx[ROOT] + tmp)
+ else max(xx[1:Ntip] + tmp)
} else x.lim <- c(1, Ntip)
- } else switch(type, "fan" = {
+ }
+ if (type == "fan") {
if (show.tip.label) {
offset <- max(nchar(x$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 (type == "unrooted") {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
- }, "radial" = {
+ }
+ if (type == "radial") {
if (show.tip.label) {
offset <- max(nchar(x$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$tip.label) * 0.03 * cex)
else -1
}
- ## mirror the xx:
- if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal) y.lim <- c(1, Ntip) else {
y.lim <- c(0, NA)
- pin2 <- par("pin")[2] # height of the device in inches
- strWi <- strwidth(x$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))$root, silent = TRUE)
- ## if the above fails, give 1/3 of the device for the tip labels:
- if (is.character(alp)) tmp <- max(yy.tips)*1.5 else {
- tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
- }
- y.lim[2] <- tmp
+ tmp <-
+ if (show.tip.label) nchar(x$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)
}
- } else switch(type, "fan" = {
+ }
+ if (type == "fan") {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
- }, "unrooted" = {
+ }
+ if (type == "unrooted") {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
- }, "radial" = {
+ }
+ if (type == "radial") {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
- })
+ }
} else if (length(y.lim) == 1) {
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal) y.lim[1] <- 1
if (type == "radial")
y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
}
- ## mirror the yy:
- if (phyloORclado && direction == "downwards") yy <- y.lim[2] - 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, ...)
+ ## fix by Klaus Schliep (2008-03-28):
+ asp <- if (type %in% c("fan", "radial")) 1 else NA
+ plot(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
+ ylab = "", xaxt = "n", yaxt = "n", bty = "n", asp = asp, ...)
if (is.null(adj))
- adj <- if (phyloORclado && direction == "leftwards") 1 else 0
- if (phyloORclado && show.tip.label) {
+ adj <- if (phyloORclado && direction == "leftwards") 1 else 0
+ if (phyloORclado) {
MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
- loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
+ loy <- 0
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
- #xx <- xx + MAXSTRING
+ loy <- 0
+ xx <- xx + MAXSTRING
}
if (!horizontal) {
psr <- par("usr")
- MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
+ MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3]) / (psr[2] - psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
- ##yy <- yy + MAXSTRING
+ yy <- yy + MAXSTRING
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
- horizontal, edge.color, edge.width, edge.lty)
+ horizontal, edge.color, edge.width)
} 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 (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 (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)
adj <- as.numeric(abs(XY$axe) > pi/2)
srt <- 180*XY$axe/pi
srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
- ## `srt' takes only a single value, so can't vectorize this:
+ ## <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:
for (i in 1:Ntip)
text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
font = font, srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
- xx.tips <- xx[1:Ntip]
- ## using atan2 considerably facilitates things compared to acos...
- angle <- atan2(yy[1:Ntip], xx.tips)*180/pi
- s <- xx.tips < 0
- angle[s] <- angle[s] + 180
+ xx.scaled <- xx[1:Ntip]
+ if (type == "fan") { # no need if type == "radial"
+ maxx <- max(abs(xx.scaled))
+ if (maxx > 1) xx.scaled <- xx.scaled/maxx
+ }
+ angle <- acos(xx.scaled)*180/pi
+ s1 <- angle > 90 & yy[1:Ntip] > 0
+ s2 <- angle < 90 & yy[1:Ntip] < 0
+ s3 <- angle > 90 & yy[1:Ntip] < 0
+ angle[s1] <- angle[s1] + 180
+ angle[s2] <- -angle[s2]
+ angle[s3] <- 180 - angle[s3]
adj <- numeric(Ntip)
- adj[xx.tips < 0] <- 1
- ## `srt' takes only a single value, so can't vectorize this:
+ adj[xx[1:Ntip] < 0] <- 1
+ ## `srt' takes only a single value, so we cannot vectorize this:
for (i in 1:Ntip)
- text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
- srt = angle[i], adj = adj[i], col = tip.color[i])
+ text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
+ srt = angle[i], adj = adj[i], col = tip.color[i])
}
}
if (show.node.label)
invisible(L)
}
-phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
- edge.color, edge.width, edge.lty)
+phylogram.plot <- function(edge, Ntip, Nnode, xx, yy,
+ horizontal, edge.color, edge.width)
{
nodes <- (Ntip + 1):(Ntip + Nnode)
if (!horizontal) {
## un trait vertical à 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]
+ j <- edge[which(edge[, 1] == i), 2]
+ y0v[i - Ntip] <- min(yy[j])
+ y1v[i - Ntip] <- max(yy[j])
}
## ... 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)
+ 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]]
- 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)
+ e.w <- unique(edge.width)
+ if (length(e.w) == 1) width.v <- rep(e.w, Nnode)
+ else {
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]
- }
- }
+ 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 {
+ color.v <- rep("black", 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
}
}
+ ## we need to reorder `edge.color' and `edge.width':
+ edge.width <- edge.width[pos]
+ edge.color <- edge.color[pos]
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
+ 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
} 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
+ 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
}
}
-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)
+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)
circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta,
- r, edge.color, edge.width, edge.lty)
-### 'edge' must be in pruningwise order
+ r, edge.color, edge.width)
{
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
+ x0 <- r0*cos(theta0)
+ y0 <- r0*sin(theta0)
+ x1 <- r1*cos(theta0)
+ y1 <- r1*sin(theta0)
- segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width, lty = edge.lty)
+ segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width)
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)
+ end <- c(tmp, dim(edge)[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])
+ 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)
}
}
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
+unrooted.xy <- function(Ntip, Nnode, edge, edge.length)
{
foo <- function(node, ANGLE, AXIS) {
ind <- which(edge[, 1] == node)
for (i in sons)
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...
- foo(Ntip + 1L, 2*pi, 0)
+ ## xx[root] <- yy[root] <- 0 # already set!
+ foo(root, 2*pi, 0)
M <- cbind(xx, yy)
axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
projects / ape.git / blobdiff