removing evolve.phylo + bug fix in as.phylo.hclust

[ape.git] / R / plot.ancestral.R

diff --git a/R/plot.ancestral.R b/R/plot.ancestral.R
deleted file mode 100644 (file)
index a53fb1b..0000000
--- a/R/plot.ancestral.R
+++ /dev/null
@@ -1,34 +0,0 @@
-## plot.ancestral.R (2005-12-04)
-
-##   Plotting Ancestral Characters on a Tree
-
-## Copyright 2005 Julien Dutheil
-
-## This file is part of the R-package `ape'.
-## See the file ../COPYING for licensing issues.
-
-plot.ancestral <- function(x, which=names(x$node.character),
-    n.col=10, col.fun=function(n) rainbow(n, start=0.4, end=0),
-    plot.node.values=FALSE,
-    ask = prod(par("mfcol")) < length(which) && dev.interactive(),
-    ...)
-{
-  if (!("ancestral" %in% class(x)))
-      stop("object \"phy\" is not of class \"ancestral\"")
-  states <- rbind(x$node.character, x$tip.character)
-  cols <- col.fun(n.col)
-  if(ask) {
-    op <- par(ask = TRUE)
-    on.exit(par(op))
-  }
-  for(state in which) {
-    a <- states[x$edge[,2],state]
-    b <- round((n.col-1)*(a-min(a))/(max(a)-min(a)))+1
-    if(plot.node.values) {
-      x$node.label <- x$node.character[,state]
-      plot.phylo(x, edge.color=cols[b], show.node.label=TRUE, sub=state, ...)
-    } else {
-      plot.phylo(x, edge.color=cols[b], sub=state, ...)
-    }
-  }
-}