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## bind.tree.R (2020-10-25)
## Bind Trees
## Copyright 2003-2020 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
`+.phylo` <- function(x, y)
{
p <- if (is.null(x$root.edge)) 0 else x$root.edge
bind.tree(x, y, position = p)
}
bind.tree <- function(x, y, where = "root", position = 0, interactive = FALSE)
{
nx <- length(x$tip.label)
mx <- x$Nnode
ROOTx <- nx + 1L
ny <- length(y$tip.label)
my <- y$Nnode
if (interactive) {
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
if (lastPP$type != "phylogram" || lastPP$direction != "rightwards")
stop("you must plot tree 'x' as a 'rightward phylogram'")
cat("Click where you want to graft tree 'y'...\n")
xy <- locator(1)
d <- abs(xy$y - lastPP$yy)
d[lastPP$xx - xy$x < 0] <- Inf
where <- which.min(d)
position <- lastPP$xx[where] - xy$x
if (position < 0) position <- 0
cat("The following parameters are used:\n")
cat(" where =", where, " position =", position, "\n")
} else {
if (where == 0 || where == "root") where <- ROOTx
if (position < 0) position <- 0
if (where > nx + mx)
stop("argument 'where' out of range for tree 'x'")
}
## check whether both trees have branch lengths:
switch(is.null(x$edge.length) + is.null(y$edge.length) + 1L,
wbl <- TRUE, {
x$edge.length <- y$edge.length <- NULL
wbl <- FALSE
warning("one tree has no branch lengths, they have been ignored")
},
wbl <- FALSE)
yHasNoRootEdge <- is.null(y$root.edge)
xHasNoRootEdge <- is.null(x$root.edge)
x <- reorder(x) # fix by Veronika Boskova
y <- reorder(y)
## find the row of 'where' before renumbering
if (where == ROOTx) case <- 1 else {
i <- which(x$edge[, 2] == where)
case <- if (where <= nx) 2 else 3
}
## case = 1 -> y is bound on the root of x
## case = 2 -> y is bound on a tip of x
## case = 3 -> y is bound on a node of x
## check that 'position' is correct
if (position && wbl) {
### New in ape 3.0-1: this makes possible binding 'y' below
### a node of 'x' thus creating a new node in 'x'
### if (!wbl)
### stop("'position' is non-null but trees have no branch lengths")
if (case == 1) {
if (xHasNoRootEdge)
stop("tree 'x' has no root edge")
if (position > x$root.edge)
stop("'position' is larger than x's root edge")
} else {
if (x$edge.length[i] < position)
stop("'position' is larger than the branch length")
}
}
## the special case of substituting two tips:
if (case == 2 && ny == 1 && !position) {
x$tip.label[x$edge[i, 2]] <- y$tip.label
if (wbl)
x$edge.length[i] <- x$edge.length[i] + y$edge.length
return(x)
}
### because in all situations internal nodes need to be
### renumbered, they are changed to negatives first, and
### nodes eventually added will be numbered sequentially
nodes <- x$edge > nx
x$edge[nodes] <- -(x$edge[nodes] - nx) # -1, ..., -mx
nodes <- y$edge > ny
y$edge[nodes] <- -(y$edge[nodes] - ny + mx) # -(mx+1), ..., -(mx+my)
ROOT <- -1L # may change later
next.node <- -(mx + my) - 1L
## renumber now the tips in y:
new.nx <- if (where <= nx && !position) nx - 1L else nx
y$edge[!nodes] <- y$edge[!nodes] + new.nx
## if 'y' as a root edge, use it:
if (!yHasNoRootEdge) {
y$edge <- rbind(c(0, y$edge[1]), y$edge)
## ^ will be filled later
next.node <- next.node - 1L
if (wbl) y$edge.length <- c(y$root.edge, y$edge.length)
}
switch(case, { # case = 1
if (position) {
x$root.edge <- x$root.edge - position
x$edge <- rbind(c(next.node, x$edge[1]), x$edge)
ROOT <- next.node
if (wbl) x$edge.length <- c(position, x$edge.length)
}
if (yHasNoRootEdge) {
j <- which(y$edge[, 1] == y$edge[1])
y$edge[j, 1] <- ROOT
} else y$edge[1] <- ROOT
x$edge <- rbind(x$edge, y$edge)
if (wbl)
x$edge.length <- c(x$edge.length, y$edge.length)
}, { # case = 2
if (position) {
x$edge[i, 2] <- next.node
x$edge <- rbind(x$edge[1:i, ], c(next.node, where), x$edge[-(1:i), ])
if (wbl) {
x$edge.length[i] <- x$edge.length[i] - position
x$edge.length <- c(x$edge.length[1:i], position, x$edge.length[-(1:i)])
}
i <- i + 1L
if (yHasNoRootEdge) {
j <- which(y$edge[, 1] == y$edge[1])
y$edge[j, 1] <- x$edge[i, 1]
} else y$edge[1] <- x$edge[i, 1]
} else {
if (yHasNoRootEdge) x$edge[i, 2] <- y$edge[1]
else {
## the root edge of y is fused with the terminal edge of x
if (wbl) y$edge.length[1] <- y$edge.length[1] + x$edge.length[i]
y$edge[1] <- x$edge[i, 1]
## delete i-th edge in x:
x$edge <- x$edge[-i, ]
if (wbl) x$edge.length <- x$edge.length[-i]
i <- i - 1L
}
x$tip.label <- x$tip.label[-where]
## renumber the tips that need to:
ii <- which(x$edge[, 2] > where & x$edge[, 2] <= nx)
x$edge[ii, 2] <- x$edge[ii, 2] - 1L
}
x$edge <- rbind(x$edge[1:i, ], y$edge, x$edge[-(1:i), ])
if (wbl)
x$edge.length <- c(x$edge.length[1:i], y$edge.length, x$edge.length[-(1:i)])
}, { # case = 3
if (position) {
if (yHasNoRootEdge) {
j <- which(y$edge[, 1] == y$edge[1])
y$edge[j, 1] <- next.node
} else y$edge[1] <- next.node
x$edge <- rbind(x$edge[1:i, ], c(next.node, x$edge[i, 2]), x$edge[-(1:i), ])
x$edge[i, 2] <- next.node
if (wbl) {
x$edge.length[i] <- x$edge.length[i] - position
x$edge.length <- c(x$edge.length[1:i], position, x$edge.length[-(1:i)])
}
i <- i + 1L
} else {
if (yHasNoRootEdge) {
j <- which(y$edge[, 1] == y$edge[1])
y$edge[j, 1] <- x$edge[i, 2]
} else y$edge[1] <- x$edge[i, 2]
}
x$edge <- rbind(x$edge[1:i, ], y$edge, x$edge[-(1:i), ])
if (wbl)
x$edge.length <- c(x$edge.length[1:i], y$edge.length, x$edge.length[-(1:i)])
})
x$tip.label <- c(x$tip.label, y$tip.label)
if (is.null(x$node.label)) {
if (!is.null(y$node.label))
x$node.label <- c(rep(NA, mx), y$node.label)
} else {
x$node.label <-
if (is.null(y$node.label)) c(x$node.label, rep(NA, my))
else c(x$node.label, y$node.label)
}
n <- length(x$tip.label)
x$Nnode <- dim(x$edge)[1] + 1L - n
## update the node labels before renumbering (this adds NA for
## the added nodes, and drops the label for those deleted)
if (!is.null(x$node.label))
x$node.label <- x$node.label[sort(-unique(x$edge[, 1]))]
## renumber nodes:
newNb <- integer(x$Nnode)
newNb[-ROOT] <- n + 1L
sndcol <- x$edge[, 2] < 0
## executed from right to left, so newNb is modified before x$edge:
x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <- n + 2:x$Nnode
x$edge[, 1] <- newNb[-x$edge[, 1]]
if (!is.null(x$node.label))
x$node.label <- x$node.label[order(newNb[newNb > 0])]
attr(x, "order") <- NULL
reorder(x)
}
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