-## drop.tip.R (2009-06-23)
+## drop.tip.R (2012-11-29)
## Remove Tips in a Phylogenetic Tree
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-extract.clade <- function(phy, node, root.edge = 0)
+extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE)
{
Ntip <- length(phy$tip.label)
ROOT <- Ntip + 1
Nedge <- dim(phy$edge)[1]
wbl <- !is.null(phy$edge.length)
- if (length(node) > 1) {
- node <- node[1]
- warning("only the first value of 'node' has been considered")
- }
- if (is.character(node)) {
- if (is.null(phy$node.label))
- stop("the tree has no node labels")
- node <- which(phy$node.label %in% node) + Ntip
+ if (interactive) node <- identify(phy)$nodes else {
+ if (length(node) > 1) {
+ node <- node[1]
+ warning("only the first value of 'node' has been considered")
+ }
+ if (is.character(node)) {
+ if (is.null(phy$node.label))
+ stop("the tree has no node labels")
+ node <- which(phy$node.label %in% node) + Ntip
+ }
+ if (node <= Ntip)
+ stop("node number must be greater than the number of tips")
}
- if (node <= Ntip)
- stop("node number must be greater than the number of tips")
if (node == ROOT) return(phy)
phy <- reorder(phy) # insure it is in cladewise order
root.node <- which(phy$edge[, 2] == node)
start <- root.node + 1 # start of the clade looked for
anc <- phy$edge[root.node, 1] # the ancestor of 'node'
- next.anc <- which(phy$edge[-(1:start), 1] == anc) # find the next occurence of 'anc'
+ next.anc <- which(phy$edge[-(1:start), 1] <= anc) # find the next occurence of 'anc' or an 'older' node
keep <- if (length(next.anc)) start + 0:(next.anc[1] - 1) else start:Nedge
if (wbl) phy$edge.length <- phy$edge.length[keep]
TIPS <- phy$edge[, 2] <= Ntip
tip <- phy$edge[TIPS, 2]
- phy$tip.label <- phy$tip.label[tip]
+ ## Fix by Ludovic Mallet and Mahendra Mariadassou (2011-11-21):
+ name <- vector("character", length(tip))
+ name[order(tip)] <- phy$tip.label[tip]
+ phy$tip.label <- name
+ ## End of fix
## keep the ordering so no need to reorder tip.label:
phy$edge[TIPS, 2] <- order(tip)
if (!is.null(phy$node.label))
drop.tip <-
function(phy, tip, trim.internal = TRUE, subtree = FALSE,
- root.edge = 0, rooted = is.rooted(phy))
+ root.edge = 0, rooted = is.rooted(phy), interactive = FALSE)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
+ if (!length(tip)) return(phy)
Ntip <- length(phy$tip.label)
## find the tips to drop:
- if (is.character(tip))
- tip <- which(phy$tip.label %in% tip)
+ if (interactive) {
+ cat("Left-click close to the tips you want to drop; right-click when finished...\n")
+ xy <- locator()
+ nToDrop <- length(xy$x)
+ tip <- integer(nToDrop)
+ lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+ for (i in 1:nToDrop) {
+ d <- sqrt((xy$x[i] - lastPP$xx)^2 + (xy$y[i] - lastPP$yy)^2)
+ tip[i] <- which.min(d)
+ }
+ } else {
+ if (is.character(tip))
+ tip <- which(phy$tip.label %in% tip)
+ }
+ if (!length(tip)) return(phy)
+ if (any(tip > Ntip))
+ warning("some tip numbers were higher than the number of tips")
if (!rooted && subtree) {
phy <- root(phy, (1:Ntip)[-tip][1])
edge2 <- phy$edge[, 2] #
keep <- !logical(Nedge)
- ## find the tips to drop:
- if (is.character(tip))
- tip <- which(phy$tip.label %in% tip)
-
- if (!rooted && subtree) {
- phy <- root(phy, (1:Ntip)[-tip][1])
- root.edge <- 0
- }
-
## delete the terminal edges given by `tip':
keep[match(tip, edge2)] <- FALSE
## get the old No. of the nodes and tips that become tips:
oldNo.ofNewTips <- phy$edge[TERMS, 2]
+ ## in case some tips are dropped but kept because of 'subtree = TRUE':
+ if (subtree) {
+ i <- which(tip %in% oldNo.ofNewTips)
+ if (length(i)) {
+ phy$tip.label[tip[i]] <- "[1_tip]"
+ tip <- tip[-i]
+ }
+ }
+
n <- length(oldNo.ofNewTips) # the new number of tips in the tree
- ## assumes that the ordering of tips is unchanged:
- phy$edge[TERMS, 2] <- 1:n
+ ## the tips may not be sorted in increasing order in the
+ ## 2nd col of edge, so no need to reorder $tip.label
+ phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
+ phy$tip.label <- phy$tip.label[-tip]
## make new tip labels if necessary:
if (subtree || !trim.internal) {
- ## get the logical indices of the tips that are kept within 'oldNo.ofNewTips':
- tips.kept <- oldNo.ofNewTips <= Ntip & !(oldNo.ofNewTips %in% tip)
- new.tip.label <- character(n)
- new.tip.label[tips.kept] <- phy$tip.label[-tip]
## get the numbers of the nodes that become tips:
- node2tip <- oldNo.ofNewTips[!tips.kept]
- new.tip.label[!tips.kept] <- if (subtree) {
+ node2tip <- oldNo.ofNewTips[oldNo.ofNewTips > Ntip]
+ new.tip.label <- if (subtree) {
paste("[", N[node2tip], "_tips]", sep = "")
} else {
if (is.null(phy$node.label)) rep("NA", length(node2tip))
else phy$node.label[node2tip - Ntip]
}
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[-(node2tip - Ntip)]
- phy$tip.label <- new.tip.label
- } else phy$tip.label <- phy$tip.label[-tip]
-
- ## update node.label if needed:
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
+# if (!is.null(phy$node.label))
+# phy$node.label <- phy$node.label[-(node2tip - Ntip)]
+ phy$tip.label <- c(phy$tip.label, new.tip.label)
+ }
phy$Nnode <- dim(phy$edge)[1] - n + 1L # update phy$Nnode
## The block below renumbers the nodes so that they conform
- ## to the "phylo" format -- same as in root()
- newNb <- integer(n + phy$Nnode)
+ ## to the "phylo" format, same as in root()
+ newNb <- integer(Ntip + Nnode)
newNb[NEWROOT] <- n + 1L
sndcol <- phy$edge[, 2] > n
## executed from right to left, so newNb is modified before phy$edge:
(n + 2):(n + phy$Nnode)
phy$edge[, 1] <- newNb[phy$edge[, 1]]
storage.mode(phy$edge) <- "integer"
+ if (!is.null(phy$node.label)) # update node.label if needed
+ phy$node.label <- phy$node.label[which(newNb > 0) - Ntip]
collapse.singles(phy)
}
+
projects / ape.git / blobdiff