improvements to compar.gee + bug fix in extract.clade

[ape.git] / R / identify.phylo.R

diff --git a/R/identify.phylo.R b/R/identify.phylo.R
index 46ab427458398c59afd37ccaf53c5852930986ac..130a8788c658b35471af23895981068e9d622e58 100644 (file)
--- a/R/identify.phylo.R
+++ b/R/identify.phylo.R
@@ -1,8 +1,8 @@
-## identify.phylo.R (2007-12-14)
+## identify.phylo.R (2008-02-28)
 
 ##   Graphical Identification of Nodes and Tips
 
-## Copyright 2007 Emmanuel Paradis
+## Copyright 2008 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -10,24 +10,23 @@
 identify.phylo <- function(x, nodes = TRUE, tips = FALSE,
                            labels = FALSE, ...)
 {
+    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$yy)^2)
+    lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+    d <- sqrt((xy$x - lastPP$xx)^2 + (xy$y - lastPP$yy)^2)
     NODE <- which.min(d)
-    print(NODE)
     res <- list()
-    if (NODE <= Ntip) {
+    if (NODE <= lastPP$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
 }