a few bug fixes especially in plot.phylo()

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

diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index 631fb4dc35029d0b52f94a361cb789cf1a35e0ae..69f08660f1afa189e9461ed00f51b330d78baf71 100644 (file)
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,8 +1,8 @@
-## plot.phylo.R (2010-03-19)
+## plot.phylo.R (2011-02-11)
 
 ##   Plot Phylogenies
 
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -276,7 +276,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
         if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
         if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
     }
-    asp <- if (type %in% c("fan", "radial")) 1 else NA # fix by Klaus Schliep (2008-03-28)
+    asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
     plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
     if (is.null(adj))
         adj <- if (phyloORclado && direction == "leftwards") 1 else 0
@@ -359,9 +359,13 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
                 srt <- 180*XY$axe/pi
                 srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
                 ## `srt' takes only a single value, so can't vectorize this:
+                ## (and need to 'elongate' these vectors:)
+                font <- rep(font, length.out = Ntip)
+                tip.color <- rep(tip.color, length.out = Ntip)
+                cex <- rep(cex, length.out = Ntip)
                 for (i in 1:Ntip)
-                  text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
-                       font = font, srt = srt[i], col = tip.color[i])
+                  text(xx[i], yy[i], cex = cex[i], x$tip.label[i], adj = adj[i],
+                       font = font[i], srt = srt[i], col = tip.color[i])
             }
         }
         if (type %in% c("fan", "radial")) {
@@ -373,8 +377,12 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
             adj <- numeric(Ntip)
             adj[xx.tips < 0] <- 1
             ## `srt' takes only a single value, so can't vectorize this:
+            ## (and need to 'elongate' these vectors:)
+            font <- rep(font, length.out = Ntip)
+            tip.color <- rep(tip.color, length.out = Ntip)
+            cex <- rep(cex, length.out = Ntip)
             for (i in 1:Ntip)
-                text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
+                text(xx[i], yy[i], x$tip.label[i], font = font[i], cex = cex[i],
                      srt = angle[i], adj = adj[i], col = tip.color[i])
         }
     }