X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fplot.phylo.R;h=3fd0637295d84063afd81cbe2bea7d5509bbe7d4;hb=2653eb671caf9234635e44b895ef48b377a89a78;hp=3235300d08ff0ea0b9b2746565c9ecbde4f8c30e;hpb=5432a54c18f69a73d7f46899a60897e2d92fb857;p=ape.git

diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index 3235300..3fd0637 100644
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,26 +1,50 @@
-## plot.phylo.R (2008-02-28)
+## plot.phylo.R (2012-03-22)
 
 ##   Plot Phylogenies
 
-## Copyright 2002-2008 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
 
 ## 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, 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, rotate.tree = 0, ...)
 {
     Ntip <- length(x$tip.label)
-    if (Ntip == 1) stop("found only one tip in the tree!")
-    Nedge <- dim(x$edge)[1]
+    if (Ntip == 1) {
+        warning("found only one tip in the tree")
+        return(NULL)
+    }
     if (any(tabulate(x$edge[, 1]) == 1))
-      stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles().")
+      stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
+
+    .nodeHeight <- function(Ntip, Nnode, edge, Nedge, yy)
+        .C("node_height", as.integer(Ntip), as.integer(Nnode),
+           as.integer(edge[, 1]), as.integer(edge[, 2]),
+           as.integer(Nedge), as.double(yy),
+           DUP = FALSE, PACKAGE = "ape")[[6]]
+
+    .nodeDepth <- function(Ntip, Nnode, edge, Nedge)
+        .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+           as.integer(edge[, 1]), as.integer(edge[, 2]),
+           as.integer(Nedge), double(Ntip + Nnode),
+           DUP = FALSE, PACKAGE = "ape")[[6]]
+
+    .nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
+        .C("node_depth_edgelength", as.integer(Ntip),
+           as.integer(Nnode), as.integer(edge[, 1]),
+           as.integer(edge[, 2]), as.integer(Nedge),
+           as.double(edge.length), double(Ntip + Nnode),
+           DUP = FALSE, PACKAGE = "ape")[[7]]
+
+    Nedge <- dim(x$edge)[1]
     Nnode <- x$Nnode
     ROOT <- Ntip + 1
     type <- match.arg(type, c("phylogram", "cladogram", "fan",
@@ -28,171 +52,163 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
     direction <- match.arg(direction, c("rightwards", "leftwards",
                                         "upwards", "downwards"))
     if (is.null(x$edge.length)) use.edge.length <- FALSE
-    if (type == "unrooted" || !use.edge.length) root.edge <- FALSE
+
+    ## the order of the last two conditions is important:
+    if (type %in% c("unrooted", "radial") || !use.edge.length ||
+        is.null(x$root.edge) || !x$root.edge) root.edge <- FALSE
+    if (type == "fan" && root.edge) {
+        warning("drawing root edge with type = 'fan' is not yet supported")
+        root.edge <- FALSE
+    }
+
     phyloORclado <- type %in% c("phylogram", "cladogram")
     horizontal <- direction %in% c("rightwards", "leftwards")
+    xe <- x$edge # to save
     if (phyloORclado) {
         ## we first compute the y-coordinates of the tips.
-        ## Fix from Klaus Schliep (2007-06-16):
-        if (!is.null(attr(x, "order")))
-          if (attr(x, "order") == "pruningwise")
-            x <- reorder(x)
-        ## End of fix
+        phyOrder <- attr(x, "order")
+        ## make sure the tree is in cladewise order:
+        if (is.null(phyOrder) || phyOrder != "cladewise") {
+            x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
+            if (!identical(x$edge, xe)) {
+                ## modified from Li-San Wang's fix (2007-01-23):
+                ereorder <- match(x$edge[, 2], xe[, 2])
+                if (length(edge.color) > 1) {
+                    edge.color <- rep(edge.color, length.out = Nedge)
+                    edge.color <- edge.color[ereorder]
+                }
+                if (length(edge.width) > 1) {
+                    edge.width <- rep(edge.width, length.out = Nedge)
+                    edge.width <- edge.width[ereorder]
+                }
+                if (length(edge.lty) > 1) {
+                    edge.lty <- rep(edge.lty, length.out = Nedge)
+                    edge.lty <- edge.lty[ereorder]
+                }
+            }
+        }
+### By contrats to ape (< 2.4), the arguments edge.color, etc., are
+### not elongated before being passed to segments(), except if needed
+### to be reordered
         yy <- numeric(Ntip + Nnode)
         TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
         yy[TIPS] <- 1:Ntip
     }
-    edge.color <- rep(edge.color, length.out = Nedge)
-    edge.width <- rep(edge.width, length.out = Nedge)
-    ## fix from Li-San Wang (2007-01-23):
-    xe <- x$edge
-    x <- reorder(x, order = "pruningwise")
-    ereorder <- match(x$edge[, 2], xe[, 2])
-    edge.color <- edge.color[ereorder]
-    edge.width <- edge.width[ereorder]
-    ## End of fix
+    ## 'z' is the tree in pruningwise order used in calls to .C
+    z <- reorder(x, order = "pruningwise")
+
     if (phyloORclado) {
         if (is.null(node.pos)) {
             node.pos <- 1
             if (type == "cladogram" && !use.edge.length) node.pos <- 2
         }
         if (node.pos == 1)
-          yy <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-                   as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                   as.integer(Nedge), as.double(yy),
-                   DUP = FALSE, PACKAGE = "ape")[[6]]
+            yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
         else {
           ## node_height_clado requires the number of descendants
           ## for each node, so we compute `xx' at the same time
           ans <- .C("node_height_clado", as.integer(Ntip),
-                    as.integer(Nnode), as.integer(x$edge[, 1]),
-                    as.integer(x$edge[, 2]), as.integer(Nedge),
+                    as.integer(Nnode), as.integer(z$edge[, 1]),
+                    as.integer(z$edge[, 2]), as.integer(Nedge),
                     double(Ntip + Nnode), as.double(yy),
                     DUP = FALSE, PACKAGE = "ape")
           xx <- ans[[6]] - 1
           yy <- ans[[7]]
         }
         if (!use.edge.length) {
-            if(node.pos != 2)
-              xx <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-                       as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                       as.integer(Nedge), double(Ntip + Nnode),
-                       DUP = FALSE, PACKAGE = "ape")[[6]] - 1
+            if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) - 1
             xx <- max(xx) - xx
         } else  {
-              xx <- .C("node_depth_edgelength", as.integer(Ntip),
-                       as.integer(Nnode), as.integer(x$edge[, 1]),
-                       as.integer(x$edge[, 2]), as.integer(Nedge),
-                       as.double(x$edge.length), double(Ntip + Nnode),
-                       DUP = FALSE, PACKAGE = "ape")[[7]]
+            xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
         }
-    }
-    if (type == "fan") {
+    } else {
+    rotate.tree <- 2 * pi * rotate.tree/360
+    switch(type, "fan" = {
         ## if the tips are not in the same order in tip.label
         ## and in edge[, 2], we must reorder the angles: we
         ## use `xx' to store temporarily the angles
-        TIPS <- xe[which(xe[, 2] <= Ntip), 2]
+        TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
         xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
         theta <- double(Ntip)
         theta[TIPS] <- xx
         theta <- c(theta, numeric(Nnode))
-        theta <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-                  as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                  as.integer(Nedge), theta, DUP = FALSE,
-                  PACKAGE = "ape")[[6]]
+        theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
         if (use.edge.length) {
-            r <- .C("node_depth_edgelength", as.integer(Ntip),
-                    as.integer(Nnode), as.integer(x$edge[, 1]),
-                    as.integer(x$edge[, 2]), as.integer(Nedge),
-                    as.double(x$edge.length), double(Ntip + Nnode),
-                    DUP = FALSE, PACKAGE = "ape")[[7]]
+            r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
         } else {
-            r <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-                    as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                    as.integer(Nedge), double(Ntip + Nnode),
-                    DUP = FALSE, PACKAGE = "ape")[[6]]
+            r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
             r <- 1/r
         }
+        theta <- theta + rotate.tree
         xx <- r*cos(theta)
         yy <- r*sin(theta)
-
-    }
-    if (type == "unrooted") {
+    }, "unrooted" = {
+        nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
         XY <- if (use.edge.length)
-          unrooted.xy(Ntip, Nnode, x$edge, x$edge.length)
+            unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree)
         else
-          unrooted.xy(Ntip, Nnode, x$edge, rep(1, Nedge))
+            unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp, rotate.tree)
         ## rescale so that we have only positive values
         xx <- XY$M[, 1] - min(XY$M[, 1])
         yy <- XY$M[, 2] - min(XY$M[, 2])
-    }
-    if (type == "radial") {
-        X <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-                as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                as.integer(Nedge), double(Ntip + Nnode),
-                DUP = FALSE, PACKAGE = "ape")[[6]]
+    }, "radial" = {
+        X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
         X[X == 1] <- 0
         ## radius:
         X <- 1 - X/Ntip
         ## angle (1st compute the angles for the tips):
         yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
-        Y <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-                as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-                as.integer(Nedge), as.double(yy),
-                DUP = FALSE, PACKAGE = "ape")[[6]]
-        xx <- X * cos(Y)
-        yy <- X * sin(Y)
-    }
-    if (phyloORclado && direction != "rightwards") {
-        if (direction == "leftwards") {
-            xx <- -xx
-            xx <- xx - min(xx)
-        }
+        Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
+        xx <- X * cos(Y + rotate.tree)
+        yy <- X * sin(Y + rotate.tree)
+    })}
+    if (phyloORclado) {
         if (!horizontal) {
             tmp <- yy
             yy <- xx
             xx <- tmp - min(tmp) + 1
-            if (direction == "downwards") {
-                yy <- -yy
-                yy <- yy - min(yy)
-            }
         }
-    }
-    if (phyloORclado && root.edge) {
-        if (direction == "rightwards") xx <- xx + x$root.edge
-        if (direction == "upwards") yy <- yy + x$root.edge
+        if (root.edge) {
+            if (direction == "rightwards") xx <- xx + x$root.edge
+            if (direction == "upwards") yy <- yy + x$root.edge
+        }
     }
     if (no.margin) par(mai = rep(0, 4))
     if (is.null(x.lim)) {
         if (phyloORclado) {
             if (horizontal) {
                 x.lim <- c(0, NA)
-                tmp <-
-                  if (show.tip.label) nchar(x$tip.label) * 0.018 * max(xx) * cex
-                  else 0
-                x.lim[2] <-
-                  if (direction == "leftwards") max(xx[ROOT] + tmp)
-                  else max(xx[1:Ntip] + tmp)
+                pin1 <- par("pin")[1] # width of the device in inches
+                strWi <- strwidth(x$tip.label, "inches") # id. for the tip labels
+                ## 1.04 comes from that we are using a regular axis system
+                ## with 4% on both sides of the range of x:
+                xx.tips <- xx[1:Ntip] * 1.04
+                ## 'alp' is the conversion coefficient from
+                ## user coordinates to inches:
+                alp <- try(uniroot(function(a) max(a*xx.tips + strWi) - pin1,
+                                   c(0, 1e6))$root, silent = TRUE)
+                ## if the above fails, give 1/3 of the device for the tip labels:
+                if (is.character(alp)) tmp <- max(xx.tips)*1.5 else {
+                    tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
+                }
+                x.lim[2] <- tmp
             } else x.lim <- c(1, Ntip)
-        }
-        if (type == "fan") {
+        } else switch(type, "fan" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 x.lim <- c(min(xx) - offset, max(xx) + offset)
             } else x.lim <- c(min(xx), max(xx))
-        }
-        if (type == "unrooted") {
+        }, "unrooted" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 x.lim <- c(0 - offset, max(xx) + offset)
             } else x.lim <- c(0, max(xx))
-        }
-        if (type == "radial") {
+        }, "radial" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.03 * cex)
                 x.lim <- c(-1 - offset, 1 + offset)
             } else x.lim <- c(-1, 1)
-        }
+        })
     } else if (length(x.lim) == 1) {
         x.lim <- c(0, x.lim)
         if (phyloORclado && !horizontal) x.lim[1] <- 1
@@ -203,86 +219,108 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
             if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
             else -1
     }
+    ## mirror the xx:
+    if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
     if (is.null(y.lim)) {
         if (phyloORclado) {
             if (horizontal) y.lim <- c(1, Ntip) else {
                 y.lim <- c(0, NA)
-                tmp <-
-                  if (show.tip.label) nchar(x$tip.label) * 0.018 * max(yy) * cex
-                  else 0
-                y.lim[2] <-
-                  if (direction == "downwards") max(yy[ROOT] + tmp)
-                  else max(yy[1:Ntip] + tmp)
+                pin2 <- par("pin")[2] # height of the device in inches
+                strWi <- strwidth(x$tip.label, "inches")
+                ## 1.04 comes from that we are using a regular axis system
+                ## with 4% on both sides of the range of x:
+                yy.tips <- yy[1:Ntip] * 1.04
+                ## 'alp' is the conversion coefficient from
+                ## user coordinates to inches:
+                alp <- try(uniroot(function(a) max(a*yy.tips + strWi) - pin2,
+                                   c(0, 1e6))$root, silent = TRUE)
+                ## if the above fails, give 1/3 of the device for the tip labels:
+                if (is.character(alp)) tmp <- max(yy.tips)*1.5 else {
+                    tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
+                }
+                y.lim[2] <- tmp
             }
-        }
-        if (type == "fan") {
+        } else switch(type, "fan" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 y.lim <- c(min(yy) - offset, max(yy) + offset)
             } else y.lim <- c(min(yy), max(yy))
-        }
-        if (type == "unrooted") {
+        }, "unrooted" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 y.lim <- c(0 - offset, max(yy) + offset)
             } else y.lim <- c(0, max(yy))
-        }
-        if (type == "radial") {
+        }, "radial" = {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.03 * cex)
                 y.lim <- c(-1 - offset, 1 + offset)
             } else y.lim <- c(-1, 1)
-        }
+        })
     } else if (length(y.lim) == 1) {
         y.lim <- c(0, y.lim)
         if (phyloORclado && horizontal) y.lim[1] <- 1
         if (type %in% c("fan", "unrooted") && show.tip.label)
-          y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
+            y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
         if (type == "radial")
-          y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
+            y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
     }
+    ## mirror the yy:
+    if (phyloORclado && direction == "downwards") yy <- max(yy) - yy
     if (phyloORclado && root.edge) {
         if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
         if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
     }
+    asp <- if (type %in% c("fan", "radial", "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, ...)
 
-    plot(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
-         ylab = "", xaxt = "n", yaxt = "n", bty = "n", ...)
+if (plot) {
     if (is.null(adj))
-      adj <- if (phyloORclado && direction == "leftwards") 1 else 0
-    if (phyloORclado) {
+        adj <- if (phyloORclado && direction == "leftwards") 1 else 0
+    if (phyloORclado && show.tip.label) {
         MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
+        loy <- 0
         if (direction == "rightwards") {
             lox <- label.offset + MAXSTRING * 1.05 * adj
-            loy <- 0
         }
         if (direction == "leftwards") {
             lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
-            loy <- 0
-            xx <- xx + MAXSTRING
+            ##xx <- xx + MAXSTRING
         }
         if (!horizontal) {
             psr <- par("usr")
-            MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3]) / (psr[2] - psr[1])
+            MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
             loy <- label.offset + MAXSTRING * 1.05 * adj
             lox <- 0
             srt <- 90 + srt
             if (direction == "downwards") {
                 loy <- -loy
-                yy <- yy + MAXSTRING
+                ##yy <- yy + MAXSTRING
                 srt <- 180 + srt
             }
         }
     }
     if (type == "phylogram") {
         phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
-                       horizontal, edge.color, edge.width)
+                       horizontal, edge.color, edge.width, edge.lty)
     } else {
-      if (type == "fan")
-        circular.plot(x$edge, Ntip, Nnode, xx, yy, theta,
-                      r, edge.color, edge.width)
-      else
-        cladogram.plot(x$edge, xx, yy, edge.color, edge.width)
+        if (type == "fan") {
+            ereorder <- match(z$edge[, 2], x$edge[, 2])
+            if (length(edge.color) > 1) {
+                edge.color <- rep(edge.color, length.out = Nedge)
+                edge.color <- edge.color[ereorder]
+            }
+            if (length(edge.width) > 1) {
+                edge.width <- rep(edge.width, length.out = Nedge)
+                edge.width <- edge.width[ereorder]
+            }
+            if (length(edge.lty) > 1) {
+                edge.lty <- rep(edge.lty, length.out = Nedge)
+                edge.lty <- edge.lty[ereorder]
+            }
+            circular.plot(z$edge, Ntip, Nnode, xx, yy, theta,
+                          r, edge.color, edge.width, edge.lty)
+        } else
+        cladogram.plot(x$edge, xx, yy, edge.color, edge.width, edge.lty)
     }
     if (root.edge)
       switch(direction,
@@ -291,11 +329,13 @@ 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$tip.label)
-        if (phyloORclado) {
+
+        if (phyloORclado)
             text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label, adj = adj,
                  font = font, srt = srt, cex = cex, col = tip.color)
-        }
+
         if (type == "unrooted") {
             if (lab4ut == "horizontal") {
                 y.adj <- x.adj <- numeric(Ntip)
@@ -307,48 +347,59 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
                 y.adj[sel] <- strheight(x$tip.label)[sel] / 2
                 sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi
                 y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
-                text(xx[1:Ntip] + x.adj*cex, yy[1:Ntip] + y.adj*cex,
+                text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex,
                      x$tip.label, adj = c(adj, 0), font = font,
                      srt = srt, cex = cex, col = tip.color)
             } else { # if lab4ut == "axial"
-                adj <- as.numeric(abs(XY$axe) > pi/2)
-                srt <- 180*XY$axe/pi
-                srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
-                ## <FIXME> temporary check of the values of `srt':
-                ## set to 0 if "-0.000001 < srt < 0"
-                sel <- srt > -1e-6 & srt < 0
-                if (any(sel)) srt[sel] <- 0
-                ## </FIXME>
-                ## `srt' takes only a single value, so we cannot vectorize this:
+                adj <- abs(XY$axe) > pi/2
+                srt <- 180 * XY$axe / pi
+                srt[adj] <- srt[adj] - 180
+                adj <- as.numeric(adj)
+                xx.tips <- xx[1:Ntip]
+                yy.tips <- yy[1:Ntip]
+                if (label.offset) {
+                    xx.tips <- xx.tips + label.offset * cos(XY$axe)
+                    yy.tips <- yy.tips + label.offset * sin(XY$axe)
+                }
+                ## `srt' takes only a single value, so can't vectorize this:
+                ## (and need to 'elongate' these vectors:)
+                font <- rep(font, length.out = Ntip)
+                tip.color <- rep(tip.color, length.out = Ntip)
+                cex <- rep(cex, length.out = Ntip)
                 for (i in 1:Ntip)
-                  text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
-                       font = font, srt = srt[i], col = tip.color[i])
+                    text(xx.tips[i], yy.tips[i], cex = cex[i],
+                         x$tip.label[i], adj = adj[i], font = font[i],
+                         srt = srt[i], col = tip.color[i])
             }
         }
         if (type %in% c("fan", "radial")) {
-            xx.scaled <- xx[1:Ntip]
-            if (type == "fan") { # no need if type == "radial"
-                maxx <- max(xx.scaled)
-                if (maxx > 1) xx.scaled <- xx.scaled/maxx
+            xx.tips <- xx[1:Ntip]
+            yy.tips <- yy[1:Ntip]
+            ## using atan2 considerably facilitates things compared to acos...
+            angle <- atan2(yy.tips, xx.tips) # in radians
+            if (label.offset) {
+                xx.tips <- xx.tips + label.offset * cos(angle)
+                yy.tips <- yy.tips + label.offset * sin(angle)
             }
-            angle <- acos(xx.scaled)*180/pi
-            s1 <- angle > 90 & yy[1:Ntip] > 0
-            s2 <- angle < 90 & yy[1:Ntip] < 0
-            s3 <- angle > 90 & yy[1:Ntip] < 0
-            angle[s1] <- angle[s1] + 180
-            angle[s2] <- -angle[s2]
-            angle[s3] <- 180 - angle[s3]
-            adj <- numeric(Ntip)
-            adj[xx[1:Ntip] < 0] <- 1
-            ## `srt' takes only a single value, so we cannot vectorize this:
+            s <- xx.tips < 0
+            angle <- angle * 180/pi # switch to degrees
+            angle[s] <- angle[s] + 180
+            adj <- as.numeric(s)
+            ## `srt' takes only a single value, so can't vectorize this:
+            ## (and need to 'elongate' these vectors:)
+            font <- rep(font, length.out = Ntip)
+            tip.color <- rep(tip.color, length.out = Ntip)
+            cex <- rep(cex, length.out = Ntip)
             for (i in 1:Ntip)
-              text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
-                   srt = angle[i], adj = adj[i], col = tip.color[i])
+                text(xx.tips[i], yy.tips[i], x$tip.label[i], font = font[i],
+                     cex = cex[i], srt = angle[i], adj = adj[i],
+                     col = tip.color[i])
         }
     }
     if (show.node.label)
-      text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
-           x$node.label, adj = adj, font = font, srt = srt, cex = cex)
+        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,
@@ -361,8 +412,8 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
     invisible(L)
 }
 
-phylogram.plot <- function(edge, Ntip, Nnode, xx, yy,
-                           horizontal, edge.color, edge.width)
+phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
+                           edge.color, edge.width, edge.lty)
 {
     nodes <- (Ntip + 1):(Ntip + Nnode)
     if (!horizontal) {
@@ -373,90 +424,134 @@ phylogram.plot <- function(edge, Ntip, Nnode, xx, yy,
     ## un trait vertical à chaque noeud...
     x0v <- xx[nodes]
     y0v <- y1v <- numeric(Nnode)
+    ## store the index of each node in the 1st column of edge:
+    NodeInEdge1 <- vector("list", Nnode)
     for (i in nodes) {
-        j <- edge[which(edge[, 1] == i), 2]
-        y0v[i - Ntip] <- min(yy[j])
-        y1v[i - Ntip] <- max(yy[j])
+        ii <- i - Ntip
+        j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
+        tmp <- range(yy[edge[j, 2]])
+        y0v[ii] <- tmp[1]
+        y1v[ii] <- tmp[2]
     }
     ## ... et un trait horizontal partant de chaque tip et chaque noeud
     ##  vers la racine
-    sq <- if (Nnode == 1) 1:Ntip else c(1:Ntip, nodes[-1])
-    y0h <- yy[sq]
-    x1h <- xx[sq]
-    ## match() is very useful here becoz each element in edge[, 2] is
-    ## unique (not sure this is so useful in edge[, 1]; needs to be checked)
-    ## `pos' gives for each element in `sq' its index in edge[, 2]
-    pos <- match(sq, edge[, 2])
-    x0h <- xx[edge[pos, 1]]
-
-    e.w <- unique(edge.width)
-    if (length(e.w) == 1) width.v <- rep(e.w, Nnode)
-    else {
-        width.v <- rep(1, Nnode)
-        for (i in 1:Nnode) {
-            br <- edge[which(edge[, 1] == i + Ntip), 2]
-            width <- unique(edge.width[br])
-            if (length(width) == 1) width.v[i] <- width
-        }
-    }
-    e.c <- unique(edge.color)
-    if (length(e.c) == 1) color.v <- rep(e.c, Nnode)
-    else {
+    x0h <- xx[edge[, 1]]
+    x1h <- xx[edge[, 2]]
+    y0h <- yy[edge[, 2]]
+
+    nc <- length(edge.color)
+    nw <- length(edge.width)
+    nl <- length(edge.lty)
+
+    if (nc + nw + nl == 3) {
+        color.v <- edge.color
+        width.v <- edge.width
+        lty.v <- edge.lty
+    } else {
+        Nedge <- dim(edge)[1]
+        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, stringsAsFactors = FALSE)
         color.v <- rep("black", Nnode)
+        width.v <- rep(1, Nnode)
+        lty.v <- rep(1, Nnode)
         for (i in 1:Nnode) {
-            br <- which(edge[, 1] == i + Ntip)
-            #br <- edge[which(edge[, 1] == i + Ntip), 2]
-            color <- unique(edge.color[br])
-            if (length(color) == 1) color.v[i] <- color
+            br <- NodeInEdge1[[i]]
+            if (length(br) > 2) {
+                x <- unique(DF[br, 1])
+                if (length(x) == 1) color.v[i] <- x
+                x <- unique(DF[br, 2])
+                if (length(x) == 1) width.v[i] <- x
+                x <- unique(DF[br, 3])
+                if (length(x) == 1) lty.v[i] <- x
+            } else {
+                A <- br[1]
+                B <- br[2]
+                if (any(DF[A, ] != DF[B, ])) {
+                    color.v[i] <- edge.color[B]
+                    width.v[i] <- edge.width[B]
+                    lty.v[i] <- edge.lty[B]
+                    ## add a new line:
+                    y0v <- c(y0v, y0v[i])
+                    y1v <- c(y1v, yy[i + Ntip])
+                    x0v <- c(x0v, x0v[i])
+                    color.v <- c(color.v, edge.color[A])
+                    width.v <- c(width.v, edge.width[A])
+                    lty.v <- c(lty.v, edge.lty[A])
+                    ## shorten the line:
+                    y0v[i] <- yy[i + Ntip]
+                } else {
+                    color.v[i] <- edge.color[A]
+                    width.v[i] <- edge.width[A]
+                    lty.v[i] <- edge.lty[A]
+                }
+            }
         }
     }
 
-    ## we need to reorder `edge.color' and `edge.width':
-    edge.width <- edge.width[pos]
-    edge.color <- edge.color[pos]
     if (horizontal) {
-        segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v) # draws vertical lines
-        segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width) # draws horizontal lines
+        segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws horizontal lines
+        segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v, lty = lty.v) # draws vertical lines
     } else {
-        segments(y0v, x0v, y1v, x0v, col = color.v, lwd = width.v) # draws horizontal lines
-        segments(y0h, x0h, y0h, x1h, col = edge.color, lwd = edge.width) # draws vertical lines
+        segments(y0h, x0h, y0h, x1h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws vertical lines
+        segments(y0v, x0v, y1v, x0v, col = color.v, lwd = width.v, lty = lty.v) # draws horizontal lines
     }
 }
 
-cladogram.plot <- function(edge, xx, yy, edge.color, edge.width)
-  segments(xx[edge[, 1]], yy[edge[, 1]], xx[edge[, 2]], yy[edge[, 2]],
-           col = edge.color, lwd = edge.width)
+cladogram.plot <- function(edge, xx, yy, edge.color, edge.width, edge.lty)
+    segments(xx[edge[, 1]], yy[edge[, 1]], xx[edge[, 2]], yy[edge[, 2]],
+             col = edge.color, lwd = edge.width, lty = edge.lty)
 
 circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta,
-                          r, edge.color, edge.width)
+                          r, edge.color, edge.width, edge.lty)
+### 'edge' must be in pruningwise order
 {
     r0 <- r[edge[, 1]]
     r1 <- r[edge[, 2]]
     theta0 <- theta[edge[, 2]]
+    costheta0 <- cos(theta0)
+    sintheta0 <- sin(theta0)
 
-    x0 <- r0*cos(theta0)
-    y0 <- r0*sin(theta0)
-    x1 <- r1*cos(theta0)
-    y1 <- r1*sin(theta0)
+    x0 <- r0 * costheta0
+    y0 <- r0 * sintheta0
+    x1 <- r1 * costheta0
+    y1 <- r1 * sintheta0
 
-    segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width)
+    segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width, lty = edge.lty)
 
     tmp <- which(diff(edge[, 1]) != 0)
     start <- c(1, tmp + 1)
-    end <- c(tmp, dim(edge)[1])
+    Nedge <- dim(edge)[1]
+    end <- c(tmp, Nedge)
+
+    ## function dispatching the features to the arcs
+    foo <- function(edge.feat, default) {
+        if (length(edge.feat) == 1) return(rep(edge.feat, Nnode))
+        else {
+            edge.feat <- rep(edge.feat, length.out = Nedge)
+            feat.arc <- rep(default, Nnode)
+            for (k in 1:Nnode) {
+                tmp <- edge.feat[start[k]]
+                if (tmp == edge.feat[end[k]]) feat.arc[k] <- tmp
+            }
+        }
+        feat.arc
+    }
+    co <- foo(edge.color, "black")
+    lw <- foo(edge.width, 1)
+    ly <- foo(edge.lty, 1)
 
     for (k in 1:Nnode) {
         i <- start[k]
         j <- end[k]
         X <- rep(r[edge[i, 1]], 100)
         Y <- seq(theta[edge[i, 2]], theta[edge[j, 2]], length.out = 100)
-        co <- if (edge.color[i] == edge.color[j]) edge.color[i] else "black"
-        lw <- if (edge.width[i] == edge.width[j]) edge.width[i] else 1
-        lines(X*cos(Y), X*sin(Y), col = co, lwd = lw)
+        lines(X*cos(Y), X*sin(Y), col = co[k], lwd = lw[k], lty = ly[k])
     }
 }
 
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length)
+unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree)
 {
     foo <- function(node, ANGLE, AXIS) {
         ind <- which(edge[, 1] == node)
@@ -471,21 +566,15 @@ unrooted.xy <- function(Ntip, Nnode, edge, edge.length)
             yy[sons[i]] <<- h*sin(beta) + yy[node]
         }
         for (i in sons)
-          if (i > Ntip) foo(i, angle[i], axis[i])
+            if (i > Ntip) foo(i, angle[i], axis[i])
     }
-    root <- Ntip + 1
     Nedge <- dim(edge)[1]
     yy <- xx <- numeric(Ntip + Nnode)
-    nb.sp <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-                as.integer(edge[, 1]), as.integer(edge[, 2]),
-                as.integer(Nedge), double(Ntip + Nnode),
-                DUP = FALSE, PACKAGE = "ape")[[6]]
     ## `angle': the angle allocated to each node wrt their nb of tips
     ## `axis': the axis of each branch
     axis <- angle <- numeric(Ntip + Nnode)
     ## start with the root...
-    ## xx[root] <- yy[root] <- 0 # already set!
-    foo(root, 2*pi, 0)
+    foo(Ntip + 1L, 2*pi, 0 + rotate.tree)
 
     M <- cbind(xx, yy)
     axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
@@ -517,3 +606,78 @@ 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 ;)
+}