-## drop.tip.R (2009-07-06)
+## drop.tip.R (2010-02-11)
## Remove Tips in a Phylogenetic Tree
-## Copyright 2003-2009 Emmanuel Paradis
+## Copyright 2003-2010 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$edge[, 2] == node)
drop.tip <-
function(phy, tip, trim.internal = TRUE, subtree = FALSE,
- root.edge = 0, rooted = is.rooted(phy))
+ root.edge = 0, rooted = is.rooted(phy), interactive = FALSE)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
Ntip <- length(phy$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$tip.label %in% tip)
+ }
if (!rooted && subtree) {
phy <- root(phy, (1:Ntip)[-tip][1])
n <- length(oldNo.ofNewTips) # the new number of tips in the tree
- ## assumes that the ordering of tips is unchanged:
- phy$edge[TERMS, 2] <- 1:n
+ ## the tips may not be sorted in increasing order of their
+ ## in the 2nd col of edge, so no need to reorder $tip.label
+ phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
## make new tip labels if necessary:
if (subtree || !trim.internal) {