1 ## bind.tree.R (2012-02-13)
5 ## Copyright 2003-2012 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 `+.phylo` <- function(x, y)
12 p <- if (is.null(x$root.edge)) 0 else x$root.edge
13 bind.tree(x, y, position = p)
16 bind.tree <- function(x, y, where = "root", position = 0, interactive = FALSE)
18 nx <- length(x$tip.label)
21 ny <- length(y$tip.label)
25 lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
26 if (lastPP$type != "phylogram" || lastPP$direction != "rightwards")
27 stop("you must plot tree 'x' as a 'rightward phylogram'")
28 cat("Click where you want to graft tree 'y'...\n")
30 d <- abs(xy$y - lastPP$yy)
31 d[lastPP$xx - xy$x < 0] <- Inf
33 position <- lastPP$xx[where] - xy$x
34 if (position < 0) position <- 0
35 cat("The following parameters are used:\n")
36 cat(" where =", where, " position =", position, "\n")
38 if (where == 0 || where == "root") where <- ROOTx
39 if (position < 0) position <- 0
41 stop("argument 'where' out of range for tree 'x'")
44 ## check whether both trees have branch lengths:
45 switch(is.null(x$edge.length) + is.null(y$edge.length) + 1L,
47 x$edge.length <- y$edge.length <- NULL
49 warning("one tree has no branch lengths, they have been ignored")
53 yHasNoRootEdge <- is.null(y$root.edge)
54 xHasNoRootEdge <- is.null(x$root.edge)
56 ## find the row of 'where' before renumbering
57 if (where == ROOTx) case <- 1 else {
58 i <- which(x$edge[, 2] == where)
59 case <- if (where <= nx) 2 else 3
61 ## case = 1 -> y is bound on the root of x
62 ## case = 2 -> y is bound on a tip of x
63 ## case = 3 -> y is bound on a node of x
65 ## check that 'position' is correct
66 if (position && wbl) {
67 ### New in ape 3.0-1: this makes possible binding 'y' below
68 ### a node of 'x' thus creating a new node in 'x'
70 ### stop("'position' is non-null but trees have no branch lengths")
73 stop("tree 'x' has no root edge")
74 if (position > x$root.edge)
75 stop("'position' is larger than x's root edge")
77 if (x$edge.length[i] < position)
78 stop("'position' is larger than the branch length")
82 ## the special case of substituting two tips:
83 if (case == 2 && ny == 1 && !position) {
84 x$tip.label[x$edge[i, 2]] <- y$tip.label
86 x$edge.length[i] <- x$edge.length[i] + y$edge.length
93 ### because in all situations internal nodes need to be
94 ### renumbered, they are changed to negatives first, and
95 ### nodes eventually added will be numbered sequentially
98 x$edge[nodes] <- -(x$edge[nodes] - nx) # -1, ..., -mx
100 y$edge[nodes] <- -(y$edge[nodes] - ny + mx) # -(mx+1), ..., -(mx+my)
101 ROOT <- -1L # may change later
102 next.node <- -(mx + my) - 1L
104 ## renumber now the tips in y:
105 new.nx <- if (where <= nx && !position) nx - 1L else nx
106 y$edge[!nodes] <- y$edge[!nodes] + new.nx
108 ## if 'y' as a root edge, use it:
109 if (!yHasNoRootEdge) {
110 y$edge <- rbind(c(0, y$edge[1]), y$edge)
111 ## ^ will be filled later
112 next.node <- next.node - 1L
113 if (wbl) y$edge.length <- c(y$root.edge, y$edge.length)
116 switch(case, { # case = 1
118 x$root.edge <- x$root.edge - position
119 x$edge <- rbind(c(next.node, x$edge[1]), x$edge)
121 if (wbl) x$edge.length <- c(position, x$edge.length)
123 if (yHasNoRootEdge) {
124 j <- which(y$edge[, 1] == y$edge[1])
126 } else y$edge[1] <- ROOT
127 x$edge <- rbind(x$edge, y$edge)
129 x$edge.length <- c(x$edge.length, y$edge.length)
132 x$edge[i, 2] <- next.node
133 x$edge <- rbind(x$edge[1:i, ], c(next.node, where), x$edge[-(1:i), ])
135 x$edge.length[i] <- x$edge.length[i] - position
136 x$edge.length <- c(x$edge.length[1:i], position, x$edge.length[-(1:i)])
139 if (yHasNoRootEdge) {
140 j <- which(y$edge[, 1] == y$edge[1])
141 y$edge[j, 1] <- x$edge[i, 1]
142 } else y$edge[1] <- x$edge[i, 1]
144 if (yHasNoRootEdge) x$edge[i, 2] <- y$edge[1]
146 ## the root edge of y is fused with the terminal edge of x
147 if (wbl) y$edge.length[1] <- y$edge.length[1] + x$edge.length[i]
148 y$edge[1] <- x$edge[i, 1]
149 ## delete i-th edge in x:
150 x$edge <- x$edge[-i, ]
151 if (wbl) x$edge.length <- x$edge.length[-i]
154 x$tip.label <- x$tip.label[-where]
155 ## renumber the tips that need to:
156 ii <- which(x$edge[, 2] > where & x$edge[, 2] <= nx)
157 x$edge[ii, 2] <- x$edge[ii, 2] - 1L
159 x$edge <- rbind(x$edge[1:i, ], y$edge, x$edge[-(1:i), ])
161 x$edge.length <- c(x$edge.length[1:i], y$edge.length, x$edge.length[-(1:i)])
164 if (yHasNoRootEdge) {
165 j <- which(y$edge[, 1] == y$edge[1])
166 y$edge[j, 1] <- next.node
167 } else y$edge[1] <- next.node
168 x$edge <- rbind(x$edge[1:i, ], c(next.node, x$edge[i, 2]), x$edge[-(1:i), ])
169 x$edge[i, 2] <- next.node
171 x$edge.length[i] <- x$edge.length[i] - position
172 x$edge.length <- c(x$edge.length[1:i], position, x$edge.length[-(1:i)])
176 if (yHasNoRootEdge) {
177 j <- which(y$edge[, 1] == y$edge[1])
178 y$edge[j, 1] <- x$edge[i, 2]
179 } else y$edge[1] <- x$edge[i, 2]
181 x$edge <- rbind(x$edge[1:i, ], y$edge, x$edge[-(1:i), ])
183 x$edge.length <- c(x$edge.length[1:i], y$edge.length, x$edge.length[-(1:i)])
186 x$tip.label <- c(x$tip.label, y$tip.label)
188 if (is.null(x$node.label)) {
189 if (!is.null(y$node.label))
190 x$node.label <- c(rep(NA, mx), y$node.label)
193 if (is.null(y$node.label)) c(x$node.label, rep(NA, my))
194 else c(x$node.label, y$node.label)
197 n <- length(x$tip.label)
198 x$Nnode <- dim(x$edge)[1] + 1L - n
200 ## update the node labels before renumbering (this adds NA for
201 ## the added nodes, and drops the label for those deleted)
202 if (!is.null(x$node.label))
203 x$node.label <- x$node.label[sort(-unique(x$edge[, 1]))]
206 newNb <- integer(x$Nnode)
207 newNb[-ROOT] <- n + 1L
208 sndcol <- x$edge[, 2] < 0
209 ## executed from right to left, so newNb is modified before x$edge:
210 x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <- n + 2:x$Nnode
211 x$edge[, 1] <- newNb[-x$edge[, 1]]
213 if (!is.null(x$node.label))
214 x$node.label <- x$node.label[order(newNb[newNb > 0])]