-## root.R (2007-12-21)
+## root.R (2011-08-05)
## Root of Phylogenetic Trees
-## Copyright 2004-2007 Emmanuel Paradis
+## Copyright 2004-2011 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
is.rooted <- function(phy)
{
- if (!"phylo" %in% class(phy))
- stop('object "phy" is not of class "phylo"')
- if (!is.null(phy$root.edge)) return(TRUE)
+ if (!inherits(phy, "phylo"))
+ stop('object "phy" is not of class "phylo"')
+ if (!is.null(phy$root.edge)) TRUE
else
- if (tabulate(phy$edge[, 1])[length(phy$tip.label) + 1] > 2)
- return(FALSE)
- else return(TRUE)
+ if (tabulate(phy$edge[, 1])[length(phy$tip.label) + 1] > 2)
+ FALSE else TRUE
}
unroot <- function(phy)
{
- if (class(phy) != "phylo")
- stop('object "phy" is not of class "phylo"')
+ if (!inherits(phy, "phylo"))
+ stop('object "phy" is not of class "phylo"')
if (dim(phy$edge)[1] < 3)
- stop("cannot unroot a tree with two edges.")
+ stop("cannot unroot a tree with less than three edges.")
## delete FIRST the root.edge (in case this is sufficient to
## unroot the tree, i.e. there is a multichotomy at the root)
if (!is.null(phy$root.edge)) phy$root.edge <- NULL
## nodes by adding 1, except the root (this remains the
## origin of the tree).
nb.tip <- length(phy$tip.label)
- ROOT <- nb.tip + 1
+ ROOT <- nb.tip + 1L
EDGEROOT <- which(phy$edge[, 1] == ROOT)
## j: the target where to stick the edge
## i: the edge to delete
- if (phy$edge[EDGEROOT[1], 2] == ROOT + 1) {
+ if (phy$edge[EDGEROOT[1], 2] == ROOT + 1L) {
j <- EDGEROOT[2]
i <- EDGEROOT[1]
} else {
## cladewise order.
phy$edge <- phy$edge[-i, ]
nodes <- phy$edge > ROOT # renumber all nodes except the root
- phy$edge[nodes] <- phy$edge[nodes] - 1
+ phy$edge[nodes] <- phy$edge[nodes] - 1L
if (!is.null(phy$edge.length)) {
phy$edge.length[j] <- phy$edge.length[j] + phy$edge.length[i]
phy$edge.length <- phy$edge.length[-i]
}
- phy$Nnode <- phy$Nnode - 1
+ phy$Nnode <- phy$Nnode - 1L
if (!is.null(phy$node.label))
phy$node.label <- phy$node.label[-2]
phy
}
-root <- function(phy, outgroup)
+root <- function(phy, outgroup, node = NULL,
+ resolve.root = FALSE, interactive = FALSE)
{
- if (class(phy) != "phylo")
- stop('object "phy" is not of class "phylo"')
- if (is.character(outgroup))
- outgroup <- which(phy$tip.label %in% outgroup)
- nb.tip <- length(phy$tip.label)
- if (length(outgroup) == nb.tip) return(phy)
-
- ## First check that the outgroup is monophyletic--
- ## unless there's only one tip specified of course
- ROOT <- nb.tip + 1
- if (length(outgroup) > 1) {
- msg <- "the specified outgroup is not monophyletic!"
- ## If all tips in `tip' are not contiguous, then
- ## no need to go further:
- if (!all(diff(outgroup) == 1)) stop(msg)
- seq.nod <- .Call("seq_root2tip", phy$edge, nb.tip,
- phy$Nnode, PACKAGE = "ape")
- sn <- seq.nod[outgroup]
- ## We go from the root to the tips: the sequence of nodes
- ## is identical until the MRCA:
- newroot <- ROOT
- i <- 2 # we start at the 2nd position since the root
- # of the tree is a common ancestor to all tips
+ if (!inherits(phy, "phylo"))
+ stop('object "phy" is not of class "phylo"')
+ phy <- reorder(phy)
+ n <- length(phy$tip.label)
+ ROOT <- n + 1L
+ if (interactive) {
+ node <- identify(phy)$nodes
+ cat("You have set resolve.root =", resolve.root, "\n")
+ }
+ if (!is.null(node)) {
+ if (node <= n)
+ stop("incorrect node#: should be greater than the number of taxa")
+ outgroup <- NULL
+ newroot <- node
+ } else {
+ if (is.numeric(outgroup)) {
+ if (any(outgroup > n))
+ stop("incorrect taxa#: should not be greater than the number of taxa")
+ outgroup <- sort(outgroup) # used below
+ }
+ if (is.character(outgroup))
+ outgroup <- which(phy$tip.label %in% outgroup)
+ if (length(outgroup) == n) return(phy)
+
+ ## First check that the outgroup is monophyletic--
+ ## unless there's only one tip specified of course
+ if (length(outgroup) > 1) {
+ pp <- prop.part(phy)
+ ingroup <- (1:n)[-outgroup]
+ newroot <- 0L
+ for (i in 2:phy$Nnode) {
+ if (identical(pp[[i]], ingroup)) {
+ newroot <- i + n
+ break
+ }
+ if (identical(pp[[i]], outgroup)) {
+ newroot <- phy$edge[which(phy$edge[, 2] == i + n), 1]
+ break
+ }
+ }
+ if (!newroot)
+ stop("the specified outgroup is not monophyletic")
+ } else newroot <- phy$edge[which(phy$edge[, 2] == outgroup), 1]
+ }
+ N <- Nedge(phy)
+ oldNnode <- phy$Nnode
+ if (newroot == ROOT) {
+ if (resolve.root) {
+ snw <- which(phy$edge[, 1] == newroot)
+ if (length(snw) > 2) {
+ a <- snw[1]:(snw[2] - 1)
+ b <- snw[2]:N
+ newnod <- oldNnode + n + 1
+ phy$edge[snw[-1], 1] <- newnod
+ phy$edge <- rbind(phy$edge[a, ], c(ROOT, newnod),
+ phy$edge[b, ])
+ if (!is.null(phy$edge.length))
+ phy$edge.length <-
+ c(phy$edge.length[a], 0, phy$edge.length[b])
+ phy$Nnode <- phy$Nnode + 1L
+ ## node renumbering (see comments below)
+ newNb <- integer(n + oldNnode)
+ newNb[newroot] <- n + 1L
+ sndcol <- phy$edge[, 2] > n
+ phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <-
+ (n + 2):(n + phy$Nnode)
+ phy$edge[, 1] <- newNb[phy$edge[, 1]]
+ }
+ }
+ return(phy)
+ }
+
+ phy$root.edge <- NULL # just in case...
+ Nclade <- tabulate(phy$edge[, 1])[ROOT] # degree of the root node
+ ## if only 2 edges connect to the root, we have to fuse them:
+ fuseRoot <- Nclade == 2
+
+ start <- which(phy$edge[, 1] == ROOT)
+ end <- c(start[-1] - 1, N)
+ o <- integer(N)
+ INV <- logical(N)
+
+ w <- which(phy$edge[, 2] == newroot)
+ nod <- phy$edge[w, 1]
+ i <- w
+ NEXT <- 1L
+
+ ## The loop below starts from the new root and goes up in the edge
+ ## matrix reversing the edges that need to be as well as well
+ ## inverting their order. The other edges must not be changed, so
+ ## their indices are stored in `stack'.
+ ## We then bind the other edges in a straightforward way.
+
+ if (nod != ROOT) {
+ ## it is important that the 3 next lines
+ ## are inside this "if" statement
+ o[NEXT] <- w
+ NEXT <- NEXT + 1L
+ INV[w] <- TRUE
+ i <- w - 1L
+ stack <- 0L
repeat {
- x <- unique(unlist(lapply(sn, "[", i)))
- if (length(x) != 1) break
- newroot <- x
- i <- i + 1
+ if (phy$edge[i, 2] == nod) {
+ if (stack) {
+ o[NEXT:(NEXT + stack - 1L)] <- (i + 1L):(i + stack)
+ NEXT <- NEXT + stack
+ stack <- 0L
+ }
+ if (phy$edge[i, 1] == ROOT) break
+ o[NEXT] <- i
+ NEXT <- NEXT + 1L
+ INV[i] <- TRUE
+ nod <- phy$edge[i, 1]
+ } else stack <- stack + 1L
+ i <- i - 1L
+ }
+ }
+
+ ## we keep the edge leading to the old root if needed:
+ if (!fuseRoot) {
+ o[NEXT] <- i
+ INV[i] <- TRUE
+ NEXT <- NEXT + 1L
+ }
+
+ endOfOutgroup <- which(phy$edge[(w+1):N, 1] < newroot)[1] + w - 1
+ if (is.na(endOfOutgroup)) endOfOutgroup <- N
+ endOfClade <- end[end >= endOfOutgroup][1]
+
+ ## bind the other clades...
+ for (j in 1:Nclade) {
+ if (end[j] == endOfClade) next
+ ## do we have to fuse the two basal edges?
+ if (fuseRoot) {
+ phy$edge[start[j], 1] <- phy$edge[i, 2]
+ if (!is.null(phy$edge.length))
+ phy$edge.length[start[j]] <- phy$edge.length[start[j]] +
+ phy$edge.length[i]
+ } #else {
+ # o[NEXT] <- i#start[j]
+ # NEXT <- NEXT + 1L
+ #}
+ s <- start[j]:end[j]
+ ne <- length(s)
+ o[NEXT:(NEXT + ne - 1L)] <- s
+ NEXT <- NEXT + ne
+ }
+
+ ## possibly bind the edges below the outgroup till the end of the clade
+ if (all(endOfOutgroup != end)) {
+ j <- (endOfOutgroup + 1L):endOfClade
+ ## we must take care that the branch inversions done above
+ ## may have changed the hierarchy of clades here, so we
+ ## travel from the bottom of this series of edges
+ stack <- 0L
+ inverted <- phy$edge[INV, 1] # <- fails if ', 2]' is used
+ for (k in rev(j)) {
+ if (any(phy$edge[k, 1] == inverted)) {
+ o[NEXT] <- k
+ NEXT <- NEXT + 1L
+ if (stack){
+ o[NEXT:(NEXT + stack - 1L)] <- (k + 1L):(k + stack)
+ NEXT <- NEXT + stack
+ stack <- 0L
+ }
+ } else stack <- stack + 1L
+ }
+ }
+
+ ## ... and the outgroup
+ s <- (w + 1L):endOfOutgroup
+ ne <- length(s)
+ o[NEXT:(NEXT + ne - 1L)] <- s
+
+ if (fuseRoot) {
+ phy$Nnode <- oldNnode - 1L
+ N <- N - 1L
+ }
+ phy$edge[INV, ] <- phy$edge[INV, 2:1]
+ phy$edge <- phy$edge[o, ]
+ if (!is.null(phy$edge.length))
+ phy$edge.length <- phy$edge.length[o]
+
+ if (resolve.root) {
+ newnod <- oldNnode + n + 1
+ if (length(outgroup) == 1L) {
+ wh <- which(phy$edge[, 2] == outgroup)
+ phy$edge[1] <- newnod
+ phy$edge <-
+ rbind(c(newroot, newnod), phy$edge[-wh, ], phy$edge[wh, ])
+ snw <- which(phy$edge[, 1] == newroot)
+ phy$edge[snw[length(snw) - 1], 1] <- newnod
+ if (!is.null(phy$edge.length)) {
+ phy$edge.length <-
+ c(0, phy$edge.length[-wh], phy$edge.length[wh])
+ }
+ } else {
+ wh <- which(phy$edge[, 1] == newroot)
+ phy$edge[wh[-1], 1] <- newnod
+ s1 <- 1:(wh[2] - 1)
+ s2 <- wh[2]:N
+ phy$edge <-
+ rbind(phy$edge[s1, ], c(newroot, newnod), phy$edge[s2, ])
+ if (!is.null(phy$edge.length)) {
+ tmp <- phy$edge.length[1]
+ phy$edge.length[1] <- 0
+ phy$edge.length <-
+ c(phy$edge.length[s1], tmp, phy$edge.length[s2])
+ }
}
- ## Check that all descendants of this node
- ## are included in the outgroup
- ## (1st solution... there may be something smarter)
- desc <- which(unlist(lapply(seq.nod,
- function(x) any(x %in% newroot))))
- if (length(outgroup) != length(desc)) stop(msg)
- if (!all(sort(outgroup) == sort(desc))) stop(msg)
-
- } else newroot <- phy$edge[which(phy$edge[, 2] == outgroup), 1]
-
- if (newroot == ROOT) return(phy)
-
-### <FIXME>
-### The remaining part of the code has not been improved; this
-### does not seem obvious. This is delayed... (2006-09-23)
-### </FIXME>
-
- ## Invert all branches from the new root to the old one
- i <- which(phy$edge[, 2] == newroot)
- nod <- phy$edge[i, 1]
- while (nod != ROOT) {
- j <- which(phy$edge[, 2] == nod)
- phy$edge[i, 1] <- phy$edge[i, 2]
- phy$edge[i, 2] <- nod
- i <- j
- nod <- phy$edge[i, 1]
+ ## N <- N + 1L ... not needed
+ phy$Nnode <- phy$Nnode + 1L
}
- i.oroot <- which(phy$edge[, 1] == ROOT)
- ## Unroot the tree if there's a basal dichotomy...
- if (length(i.oroot) == 2) {
- j <- i.oroot[which(i.oroot != i)]
- phy$edge[j, 1] <- phy$edge[i, 2]
- phy$edge <- phy$edge[-i, ]
- if (!is.null(phy$edge.length)) {
- phy$edge.length[j] <- phy$edge.length[j] + phy$edge.length[i]
- phy$edge.length <- phy$edge.length[-i]
+ ## The block below renumbers the nodes so that they conform
+ ## to the "phylo" format
+ newNb <- integer(n + oldNnode)
+ newNb[newroot] <- n + 1L
+ sndcol <- phy$edge[, 2] > n
+ ## executed from right to left, so newNb is modified before phy$edge:
+ phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <-
+ (n + 2):(n + phy$Nnode)
+ phy$edge[, 1] <- newNb[phy$edge[, 1]]
+
+ if (!is.null(phy$node.label)) {
+ #browser()
+ newNb <- newNb[-(1:n)]
+ if (fuseRoot) {
+ newNb <- newNb[-1]
+ phy$node.label <- phy$node.label[-1]
+ }
+ phy$node.label <- phy$node.label[order(newNb)]
+ if (resolve.root) {
+ phy$node.label[is.na(phy$node.label)] <- phy$node.label[1]
+ phy$node.label[1] <- NA
+ ##phy$node.label <- c(phy$node.label[1], NA, phy$node.label[-1])
+ ##phy$node.label <- c("NA", phy$node.label)
}
- phy$edge[which(phy$edge == newroot)] <- ROOT
- } else {
- ## ... otherwise just invert the root with the newroot
- phy$edge[which(phy$edge == newroot)] <- ROOT
- phy$edge[i.oroot] <- newroot
- ## ... and invert finally! (fixed 2005-11-07)
- phy$edge[i, ] <- rev(phy$edge[i, ])
}
- if (!is.null(phy$node.label))
- ## It's important to not delete the label of the newroot
- ## to keep the positions of the other nodes
- phy$node.label[1] <- phy$node.label[newroot - nb.tip]
- ## Not needed: phy$Nnode <- phy$Nnode - 1
- read.tree(text = write.tree(phy))
+ phy
}
projects / ape.git / blobdiff