bug fix in chronopl()

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

diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index b2273ca2ef1679a05924abc2541aac249e556f9d..da5ebec9d1fb58e74b314da9f24dc6723dd46c28 100644 (file)
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,4 +1,4 @@
-## plot.phylo.R (2011-02-17)
+## plot.phylo.R (2011-06-14)
 
 ##   Plot Phylogenies
 
@@ -7,14 +7,15 @@
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
-plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
-                       node.pos = NULL, show.tip.label = TRUE,
-                       show.node.label = FALSE, edge.color = "black",
-                       edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
-                       adj = NULL, srt = 0, no.margin = FALSE,
-                       root.edge = FALSE, label.offset = 0, underscore = FALSE,
-                       x.lim = NULL, y.lim = NULL, direction = "rightwards",
-                       lab4ut = "horizontal", tip.color = "black", ...)
+plot.phylo <-
+    function(x, type = "phylogram", use.edge.length = TRUE,
+             node.pos = NULL, show.tip.label = TRUE,
+             show.node.label = FALSE, edge.color = "black",
+             edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
+             adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
+             label.offset = 0, underscore = FALSE, x.lim = NULL,
+             y.lim = NULL, direction = "rightwards", lab4ut = "horizontal",
+             tip.color = "black", plot = TRUE, ...)
 {
     Ntip <- length(x$tip.label)
     if (Ntip == 1) {
@@ -278,6 +279,8 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
     }
     asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
     plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
+
+if (plot) {
     if (is.null(adj))
         adj <- if (phyloORclado && direction == "leftwards") 1 else 0
     if (phyloORclado && show.tip.label) {
@@ -288,7 +291,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
         }
         if (direction == "leftwards") {
             lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
-            #xx <- xx + MAXSTRING
+            ##xx <- xx + MAXSTRING
         }
         if (!horizontal) {
             psr <- par("usr")
@@ -403,6 +406,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
     if (show.node.label)
         text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
              x$node.label, adj = adj, font = font, srt = srt, cex = cex)
+}
     L <- list(type = type, use.edge.length = use.edge.length,
               node.pos = node.pos, show.tip.label = show.tip.label,
               show.node.label = show.node.label, font = font,
@@ -609,3 +613,78 @@ plot.multiPhylo <- function(x, layout = 1, ...)
     }
     for (i in 1:length(x)) plot(x[[i]], ...)
 }
+
+trex <- function(phy, title = TRUE, subbg = "lightyellow3",
+                 return.tree = FALSE, ...)
+{
+    lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+    devmain <- dev.cur() # where the main tree is plotted
+
+    restore <- function() {
+        dev.set(devmain)
+        assign("last_plot.phylo", lastPP, envir = .PlotPhyloEnv)
+    }
+
+    on.exit(restore())
+    NEW <- TRUE
+    cat("Click close to a node. Right-click to exit.\n")
+    repeat {
+        x <- identify.phylo(phy, quiet = TRUE)
+        if (is.null(x)) return(invisible(NULL)) else {
+            x <- x$nodes
+            if (is.null(x)) cat("Try again!\n") else {
+                if (NEW) {
+                    dev.new()
+                    par(bg = subbg)
+                    devsub <- dev.cur()
+                    NEW <- FALSE
+                } else dev.set(devsub)
+
+                tr <- extract.clade(phy, x)
+                plot(tr, ...)
+                if (is.character(title)) title(title)
+                else if (title) {
+                     tl <-
+                         if (is.null(phy$node.label))
+                         paste("From node #", x, sep = "")
+                         else paste("From", phy$node.label[x - Ntip(phy)])
+                     title(tl)
+                }
+                if (return.tree) return(tr)
+                restore()
+            }
+        }
+    }
+}
+
+kronoviz <- function(x, layout = length(x), horiz = TRUE, ...)
+{
+    par(mar = rep(0.5, 4), oma = rep(2, 4))
+    rts <- sapply(x, function(x) branching.times(x)[1])
+    maxrts <- max(rts)
+    lim <- cbind(rts - maxrts, rts)
+    Ntree <- length(x)
+    Ntips <- sapply(x, Ntip)
+    if (horiz) {
+        nrow <- layout
+        w <- 1
+        h <- Ntips
+    } else {
+        nrow <- 1
+        w <- Ntips
+        h <- 1
+    }
+    layout(matrix(1:layout, nrow), widths = w, heights = h)
+    if (layout > Ntree && !par("ask")) {
+        par(ask = TRUE)
+        on.exit(par(ask = FALSE))
+    }
+    if (horiz) {
+        for (i in 1:Ntree)
+            plot(x[[i]], x.lim = lim[i, ], ...)
+    } else {
+        for (i in 1:Ntree)
+            plot(x[[i]], y.lim = lim[i, ], direction = "u", ...)
+    }
+    axisPhylo(if (horiz) 1 else 4) # better if the deepest tree is last ;)
+}