-## identify.phylo.R (2007-12-14)
+## identify.phylo.R (2011-03-23)
## Graphical Identification of Nodes and Tips
-## Copyright 2007 Emmanuel Paradis
+## Copyright 2008-2011 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
identify.phylo <- function(x, nodes = TRUE, tips = FALSE,
- labels = FALSE, ...)
+ labels = FALSE, quiet = FALSE, ...)
{
+ if (!quiet)
+ cat("Click close to a node of the tree...\n")
xy <- locator(1)
- Ntip <- .last_plot.phylo$Ntip
- d <- sqrt((xy$x - .last_plot.phylo$xx)^2 +
- (xy$y - .last_plot.phylo$yy)^2)
+ if (is.null(xy)) return(NULL)
+ lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+ ## rescale the coordinates (especially if the x- and
+ ## y-scales are very different):
+ pin <- par("pin")
+ rescaleX <- pin[1]/max(lastPP$xx)
+ xx <- rescaleX * lastPP$xx
+ rescaleY <- pin[2]/max(lastPP$yy)
+ yy <- rescaleY * lastPP$yy
+ xy$x <- rescaleX * xy$x
+ xy$y <- rescaleY * xy$y
+ ## end of rescaling
+ d <- (xy$x - xx)^2 + (xy$y - yy)^2 # no need to sqrt()
NODE <- which.min(d)
- print(NODE)
res <- list()
- if (NODE <= Ntip) {
+ if (NODE <= lastPP$Ntip) {
res$tips <- if (labels) x$tip.label[NODE] else NODE
return(res)
}
if (tips) {
- TIPS <- prop.part(x)[[NODE - Ntip]]
+ TIPS <- prop.part(x)[[NODE - lastPP$Ntip]]
res$tips <- if (labels) x$tip.label[TIPS] else TIPS
}
if (nodes) {
if (is.null(x$node.label)) labels <- FALSE
- res$nodes <- if (labels) x$node.label[NODE - Ntip] else NODE
+ res$nodes <- if (labels) x$node.label[NODE - lastPP$Ntip] else NODE
}
res
}