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 e02ba3071726ffcd8e87a6f966aff4e786bfa0eb..69f08660f1afa189e9461ed00f51b330d78baf71 100644 (file)
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,8 +1,8 @@
-## plot.phylo.R (2010-01-04)
+## 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.
@@ -198,8 +198,6 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
                     tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
                 }
                 x.lim[2] <- tmp
-                if (direction == "leftwards") xx <- x.lim[2] - xx #max(xx[ROOT] + tmp)
-#                  else max(xx[1:Ntip] + tmp)
             } else x.lim <- c(1, Ntip)
         } else switch(type, "fan" = {
             if (show.tip.label) {
@@ -227,6 +225,8 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
             if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
             else -1
     }
+    ## mirror the xx:
+    if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
     if (is.null(y.lim)) {
         if (phyloORclado) {
             if (horizontal) y.lim <- c(1, Ntip) else {
@@ -245,7 +245,6 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
                     tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
                 }
                 y.lim[2] <- tmp
-                if (direction == "downwards") yy <- y.lim[2] - yy
             }
         } else switch(type, "fan" = {
             if (show.tip.label) {
@@ -271,11 +270,13 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
         if (type == "radial")
           y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
     }
+    ## mirror the yy:
+    if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy
     if (phyloORclado && root.edge) {
         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
@@ -332,6 +333,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
              "upwards" = segments(xx[ROOT], 0, xx[ROOT], x$root.edge),
              "downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge))
     if (show.tip.label) {
+        if (is.expression(x$tip.label)) underscore <- TRUE
         if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
 
         if (phyloORclado)
@@ -357,9 +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$tip.label[i], adj = adj[i],
+                       font = font[i], srt = srt[i], col = tip.color[i])
             }
         }
         if (type %in% c("fan", "radial")) {
@@ -371,8 +377,12 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
             adj <- numeric(Ntip)
             adj[xx.tips < 0] <- 1
             ## `srt' takes only a single value, so can't vectorize this:
+            ## (and need to 'elongate' these vectors:)
+            font <- rep(font, length.out = Ntip)
+            tip.color <- rep(tip.color, length.out = Ntip)
+            cex <- rep(cex, length.out = Ntip)
             for (i in 1:Ntip)
-                text(xx[i], yy[i], x$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])
         }
     }
@@ -431,7 +441,7 @@ phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
         edge.color <- rep(edge.color, length.out = Nedge)
         edge.width <- rep(edge.width, length.out = Nedge)
         edge.lty <- rep(edge.lty, length.out = Nedge)
-        DF <- data.frame(edge.color, edge.width, edge.lty)
+        DF <- data.frame(edge.color, edge.width, edge.lty, stringsAsFactors = FALSE)
         color.v <- rep("black", Nnode)
         width.v <- rep(1, Nnode)
         lty.v <- rep(1, Nnode)