1 ## cophyloplot.R (2012-02-14)
3 ## Plots two phylogenetic trees face to
4 ## face with the links between the tips
6 ## Copyright 2008-2010 Damien de Vienne
8 ## This file is part of the R-package `ape'.
9 ## See the file ../COPYING for licensing issues.
12 function(x, y, assoc = NULL, use.edge.length = FALSE, space = 0,
13 length.line = 1, gap = 2, type = "phylogram", rotate = FALSE,
14 col = par("fg"), lwd = par("lwd"), lty = par("lty"),
15 show.tip.label = TRUE, font = 3, ...)
18 assoc <- matrix(ncol = 2)
19 print("No association matrix specified. Links will be omitted.")
22 cat("\n Click on a node to rotate (right click to exit)\n\n")
24 res <- plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
25 space = space, length.line = length.line, gap = gap,
26 type = type, return = TRUE, col = col, lwd=lwd, lty=lty, show.tip.label = show.tip.label,
28 click <- identify(res$c[, 1], res$c[, 2], n = 1)
29 if (click < length(res$a[, 1]) + 1) {
30 if (click > res$N.tip.x)
32 } else if (click < length(res$c[, 1]) + 1) {
33 if (click > length(res$a[, 1]) + res$N.tip.y)
34 y <- rotate(y, click - length(res$a[, 1]))
37 on.exit(print("done"))
39 else plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
40 space = space, length.line = length.line, gap = gap,
41 type = type, return = FALSE, col = col, lwd=lwd, lty=lty, show.tip.label = show.tip.label, font = font)
45 function (x, y, assoc = assoc, use.edge.length = use.edge.length,
46 space = space, length.line = length.line, gap = gap,
47 type = type, return = return, col = col, lwd=lwd, lty=lty,
48 show.tip.label = show.tip.label,
52 ###choice of the minimum space between the trees
53 left <- max(nchar(x$tip.label, type = "width")) + length.line
54 right <- max(nchar(y$tip.label, type = "width")) + length.line
55 space.min <- left + right + gap * 2
56 if ((space <= 0) || (space < space.min)) space <- space.min
59 res$N.tip.x <- N.tip.x
60 res$N.tip.y <- N.tip.y
61 a <- plotPhyloCoor(x, use.edge.length = use.edge.length, type = type)
63 b <- plotPhyloCoor(y, use.edge.length = use.edge.length,
64 direction = "leftwards", type = type)
65 ###for the two trees to have the extreme leaves at the same ordinate.
66 a[, 2] <- a[, 2] - min(a[, 2])
67 b[, 2] <- b[, 2] - min(b[, 2])
70 b2[, 1] <- b[1:nrow(b), 1] * (max(a[, 1])/max(b[, 1])) +
72 b2[, 2] <- b[1:nrow(b), 2] * (max(a[, 2])/max(b[, 2]))
74 c <- matrix(ncol = 2, nrow = nrow(a) + nrow(b))
75 c[1:nrow(a), ] <- a[1:nrow(a), ]
76 c[nrow(a) + 1:nrow(b), 1] <- b2[, 1]
77 c[nrow(a) + 1:nrow(b), 2] <- b2[, 2]
79 plot(c, type = "n", xlim = NULL, ylim = NULL, log = "", main = NULL,
80 sub = NULL, xlab = NULL, ylab = NULL, ann = FALSE, axes = FALSE,
82 ###segments for cladograms
83 if (type == "cladogram") {
84 for (i in 1:(nrow(a) - 1)) segments(a[x$edge[i, 1], 1],
85 a[x$edge[i, 1], 2], a[x$edge[i, 2], 1], a[x$edge[i,
87 for (i in 1:(nrow(b) - 1))
88 segments(b2[y$edge[i, 1], 1], b2[y$edge[i, 1], 2],
89 b2[y$edge[i, 2], 1], b2[y$edge[i, 2], 2])
91 ###segments for phylograms
92 if (type == "phylogram") {
93 for (i in (N.tip.x + 1):nrow(a)) {
94 l <- length(x$edge[x$edge[, 1] == i, ][, 1])
96 segments(a[x$edge[x$edge[, 1] == i, ][1, 1],
97 1], a[x$edge[x$edge[, 1] == i, 2], 2][1], a[x$edge[x$edge[,
98 1] == i, ][1, 1], 1], a[x$edge[x$edge[, 1] ==
100 segments(a[x$edge[x$edge[, 1] == i, ][1, 1],
101 1], a[x$edge[x$edge[, 1] == i, 2], 2][j], a[x$edge[x$edge[,
102 1] == i, 2], 1][j], a[x$edge[x$edge[, 1] ==
106 for (i in (N.tip.y + 1):nrow(b)) {
107 l <- length(y$edge[y$edge[, 1] == i, ][, 1])
109 segments(b2[y$edge[y$edge[, 1] == i, ][1, 1],
110 1], b2[y$edge[y$edge[, 1] == i, 2], 2][1],
111 b2[y$edge[y$edge[, 1] == i, ][1, 1], 1], b2[y$edge[y$edge[,
113 segments(b2[y$edge[y$edge[, 1] == i, ][1, 1],
114 1], b2[y$edge[y$edge[, 1] == i, 2], 2][j],
115 b2[y$edge[y$edge[, 1] == i, 2], 1][j], b2[y$edge[y$edge[,
120 if (show.tip.label) {
121 text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4,
122 labels = x$tip.label)
123 text(b2[1:N.tip.y, ], cex = 1, font = font, pos = 2,
124 labels = y$tip.label)
126 ###links between associated taxa. Takes into account the size of the character strings of the taxa names.
129 decx <- array(nrow(assoc))
130 decy <- array(nrow(assoc))
133 if (length(col)==1) colors<-c(rep(col, nrow(assoc)))
134 else if (length(col)>=nrow(assoc)) colors<-col
135 else colors<-c(rep(col, as.integer(nrow(assoc)/length(col))+1))
138 if (length(lwd)==1) lwidths<-c(rep(lwd, nrow(assoc)))
139 else if (length(lwd)>=nrow(assoc)) lwidths<-lwd
140 else lwidths<-c(rep(lwd, as.integer(nrow(assoc)/length(lwd))+1))
143 if (length(lty) == 1) ltype <- c(rep(lty, nrow(assoc)))
144 else if (length(lty) >= nrow(assoc)) ltype <- lty
145 else ltype <- c(rep(lty, as.integer(nrow(assoc)/length(lty))+1))
147 for (i in 1:nrow(assoc)) {
148 if (show.tip.label) {
149 decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == assoc[i, 1]]])
150 decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == assoc[i, 2]]])
152 decx[i] <- decy[i] <- 0
155 segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap,
156 a[lsa[x$tip.label == assoc[i, 1]], 2],
157 a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
158 a[lsa[x$tip.label == assoc[i, 1]], 2],
159 col = colors[i], lwd = lwidths[i], lty = ltype[i])
161 segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap),
162 b2[lsb[y$tip.label == assoc[i, 2]], 2],
163 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
164 b2[lsb[y$tip.label == assoc[i, 2]], 2],
165 col = colors[i], lwd = lwidths[i], lty = ltype[i])
167 segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
168 a[lsa[x$tip.label == assoc[i, 1]], 2],
169 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
170 b2[lsb[y$tip.label == assoc[i, 2]], 2],
171 col = colors[i], lwd = lwidths[i], lty = ltype[i])
173 if (return == TRUE) return(res)