X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fplot.phylo.R;h=ca3ff1ce570960fa9c86b35f0cdc93a146312da2;hb=52008daf7f708f3fcdc735f22af308dd1a461670;hp=e02ba3071726ffcd8e87a6f966aff4e786bfa0eb;hpb=3d25bf9304a2ec03022275950e4ccc720fc70675;p=ape.git

diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index e02ba30..ca3ff1c 100644
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,8 +1,8 @@
-## plot.phylo.R (2010-01-04)
+## plot.phylo.R (2008-05-08)
 
 ##   Plot Phylogenies
 
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2008 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -10,40 +10,17 @@
 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"),
+                       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", ...)
 {
     Ntip <- length(x$tip.label)
-    if (Ntip == 1) {
-        warning("found only one tip in the tree")
-        return(NULL)
-    }
-    if (any(tabulate(x$edge[, 1]) == 1))
-      stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
-
-    .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]]
-
+    if (Ntip == 1) stop("found only one tip in the tree!")
     Nedge <- dim(x$edge)[1]
+    if (any(tabulate(x$edge[, 1]) == 1))
+      stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles().")
     Nnode <- x$Nnode
     ROOT <- Ntip + 1
     type <- match.arg(type, c("phylogram", "cladogram", "fan",
@@ -51,172 +28,171 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
     direction <- match.arg(direction, c("rightwards", "leftwards",
                                         "upwards", "downwards"))
     if (is.null(x$edge.length)) use.edge.length <- FALSE
-
-    ## 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
-    }
-
+    if (type == "unrooted" || !use.edge.length) root.edge <- FALSE
     phyloORclado <- type %in% c("phylogram", "cladogram")
     horizontal <- direction %in% c("rightwards", "leftwards")
-    xe <- x$edge # to save
     if (phyloORclado) {
         ## we first compute the y-coordinates of the tips.
-        phyOrder <- attr(x, "order")
-        ## make sure the tree is in cladewise order:
-        if (is.null(phyOrder) || phyOrder != "cladewise") {
-            x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
-            if (!identical(x$edge, xe)) {
-                ## modified from Li-San Wang's fix (2007-01-23):
-                ereorder <- match(x$edge[, 2], xe[, 2])
-                if (length(edge.color) > 1) {
-                    edge.color <- rep(edge.color, length.out = Nedge)
-                    edge.color <- edge.color[ereorder]
-                }
-                if (length(edge.width) > 1) {
-                    edge.width <- rep(edge.width, length.out = Nedge)
-                    edge.width <- edge.width[ereorder]
-                }
-                if (length(edge.lty) > 1) {
-                    edge.lty <- rep(edge.lty, length.out = Nedge)
-                    edge.lty <- edge.lty[ereorder]
-                }
-            }
-        }
-### By contrats to ape (< 2.4), the arguments edge.color, etc., are
-### not elongated before being passed to segments(), except if needed
-### to be reordered
+        ## Fix from Klaus Schliep (2007-06-16):
+        if (!is.null(attr(x, "order")))
+          if (attr(x, "order") == "pruningwise")
+            x <- reorder(x)
+        ## End of fix
         yy <- numeric(Ntip + Nnode)
         TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
         yy[TIPS] <- 1:Ntip
     }
-    ## 'z' is the tree in pruningwise order used in calls to .C
-    z <- reorder(x, order = "pruningwise")
-###    edge.color <- rep(edge.color, length.out = Nedge)
-###    edge.width <- rep(edge.width, length.out = Nedge)
-###    edge.lty <- rep(edge.lty, length.out = Nedge)
-###    ## fix from Li-San Wang (2007-01-23):
-###    xe <- x$edge
-###    x <- reorder(x, order = "pruningwise")
-###    ereorder <- match(x$edge[, 2], xe[, 2])
-###    edge.color <- edge.color[ereorder]
-###    edge.width <- edge.width[ereorder]
-###    edge.lty <- edge.lty[ereorder]
-###    ## end of fix
+    edge.color <- rep(edge.color, length.out = Nedge)
+    edge.width <- rep(edge.width, length.out = Nedge)
+    ## fix from Li-San Wang (2007-01-23):
+    xe <- x$edge
+    x <- reorder(x, order = "pruningwise")
+    ereorder <- match(x$edge[, 2], xe[, 2])
+    edge.color <- edge.color[ereorder]
+    edge.width <- edge.width[ereorder]
+    ## End of fix
     if (phyloORclado) {
         if (is.null(node.pos)) {
             node.pos <- 1
             if (type == "cladogram" && !use.edge.length) node.pos <- 2
         }
         if (node.pos == 1)
-            yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
+          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]]
         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(z$edge[, 1]),
-                    as.integer(z$edge[, 2]), as.integer(Nedge),
+                    as.integer(Nnode), as.integer(x$edge[, 1]),
+                    as.integer(x$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 <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) - 1
+            if(node.pos != 2)
+              xx <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+                       as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+                       as.integer(Nedge), double(Ntip + Nnode),
+                       DUP = FALSE, PACKAGE = "ape")[[6]] - 1
             xx <- max(xx) - xx
         } else  {
-            xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
+              xx <- .C("node_depth_edgelength", as.integer(Ntip),
+                       as.integer(Nnode), as.integer(x$edge[, 1]),
+                       as.integer(x$edge[, 2]), as.integer(Nedge),
+                       as.double(x$edge.length), double(Ntip + Nnode),
+                       DUP = FALSE, PACKAGE = "ape")[[7]]
         }
-    } else switch(type, "fan" = {
+    }
+    if (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 <- x$edge[which(x$edge[, 2] <= Ntip), 2]
+        TIPS <- xe[which(xe[, 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 <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
+        theta <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
+                  as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+                  as.integer(Nedge), theta, DUP = FALSE,
+                  PACKAGE = "ape")[[6]]
         if (use.edge.length) {
-            r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
+            r <- .C("node_depth_edgelength", as.integer(Ntip),
+                    as.integer(Nnode), as.integer(x$edge[, 1]),
+                    as.integer(x$edge[, 2]), as.integer(Nedge),
+                    as.double(x$edge.length), double(Ntip + Nnode),
+                    DUP = FALSE, PACKAGE = "ape")[[7]]
         } else {
-            r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
+            r <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+                    as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+                    as.integer(Nedge), double(Ntip + Nnode),
+                    DUP = FALSE, PACKAGE = "ape")[[6]]
             r <- 1/r
         }
         xx <- r*cos(theta)
         yy <- r*sin(theta)
-    }, "unrooted" = {
-        nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
+
+    }
+    if (type == "unrooted") {
         XY <- if (use.edge.length)
-            unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp)
+          unrooted.xy(Ntip, Nnode, x$edge, x$edge.length)
         else
-            unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp)
+          unrooted.xy(Ntip, Nnode, x$edge, rep(1, Nedge))
         ## rescale so that we have only positive values
         xx <- XY$M[, 1] - min(XY$M[, 1])
         yy <- XY$M[, 2] - min(XY$M[, 2])
-    }, "radial" = {
-        X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
+    }
+    if (type == "radial") {
+        X <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
+                as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
+                as.integer(Nedge), double(Ntip + Nnode),
+                DUP = FALSE, PACKAGE = "ape")[[6]]
         X[X == 1] <- 0
         ## radius:
         X <- 1 - X/Ntip
         ## angle (1st compute the angles for the tips):
         yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
-        Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
+        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) {
+    }
+    if (phyloORclado && direction != "rightwards") {
+        if (direction == "leftwards") {
+            xx <- -xx
+            xx <- xx - min(xx)
+        }
         if (!horizontal) {
             tmp <- yy
             yy <- xx
             xx <- tmp - min(tmp) + 1
-        }
-        if (root.edge) {
-            if (direction == "rightwards") xx <- xx + x$root.edge
-            if (direction == "upwards") yy <- yy + x$root.edge
+            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 (no.margin) par(mai = rep(0, 4))
     if (is.null(x.lim)) {
         if (phyloORclado) {
             if (horizontal) {
                 x.lim <- c(0, NA)
-                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
-                if (direction == "leftwards") xx <- x.lim[2] - xx #max(xx[ROOT] + tmp)
-#                  else max(xx[1:Ntip] + tmp)
+                tmp <-
+                  if (show.tip.label) nchar(x$tip.label) * 0.018 * max(xx) * cex
+                  else 0
+                x.lim[2] <-
+                  if (direction == "leftwards") max(xx[ROOT] + tmp)
+                  else max(xx[1:Ntip] + tmp)
             } else x.lim <- c(1, Ntip)
-        } else switch(type, "fan" = {
+        }
+        if (type == "fan") {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 x.lim <- c(min(xx) - offset, max(xx) + offset)
             } else x.lim <- c(min(xx), max(xx))
-        }, "unrooted" = {
+        }
+        if (type == "unrooted") {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 x.lim <- c(0 - offset, max(xx) + offset)
             } else x.lim <- c(0, max(xx))
-        }, "radial" = {
+        }
+        if (type == "radial") {
             if (show.tip.label) {
                 offset <- max(nchar(x$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
@@ -231,38 +207,32 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
         if (phyloORclado) {
             if (horizontal) y.lim <- c(1, Ntip) else {
                 y.lim <- c(0, NA)
-                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 (direction == "downwards") yy <- y.lim[2] - yy
+                tmp <-
+                  if (show.tip.label) nchar(x$tip.label) * 0.018 * max(yy) * cex
+                  else 0
+                y.lim[2] <-
+                  if (direction == "downwards") max(yy[ROOT] + tmp)
+                  else max(yy[1:Ntip] + tmp)
             }
-        } else switch(type, "fan" = {
+        }
+        if (type == "fan") {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 y.lim <- c(min(yy) - offset, max(yy) + offset)
             } else y.lim <- c(min(yy), max(yy))
-        }, "unrooted" = {
+        }
+        if (type == "unrooted") {
             if (show.tip.label) {
                 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
                 y.lim <- c(0 - offset, max(yy) + offset)
             } else y.lim <- c(0, max(yy))
-        }, "radial" = {
+        }
+        if (type == "radial") {
             if (show.tip.label) {
                 offset <- max(nchar(x$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
@@ -275,55 +245,45 @@ 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)
-    plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
+    ## fix by Klaus Schliep (2008-03-28):
+    asp <- if (type %in% c("fan", "radial")) 1 else NA
+    plot(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
+         ylab = "", xaxt = "n", yaxt = "n", bty = "n", asp = asp, ...)
     if (is.null(adj))
-        adj <- if (phyloORclado && direction == "leftwards") 1 else 0
-    if (phyloORclado && show.tip.label) {
+      adj <- if (phyloORclado && direction == "leftwards") 1 else 0
+    if (phyloORclado) {
         MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
-        loy <- 0
         if (direction == "rightwards") {
             lox <- label.offset + MAXSTRING * 1.05 * adj
+            loy <- 0
         }
         if (direction == "leftwards") {
             lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
-            #xx <- xx + MAXSTRING
+            loy <- 0
+            xx <- xx + MAXSTRING
         }
         if (!horizontal) {
             psr <- par("usr")
-            MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
+            MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3]) / (psr[2] - psr[1])
             loy <- label.offset + MAXSTRING * 1.05 * adj
             lox <- 0
             srt <- 90 + srt
             if (direction == "downwards") {
                 loy <- -loy
-                ##yy <- yy + MAXSTRING
+                yy <- yy + MAXSTRING
                 srt <- 180 + srt
             }
         }
     }
     if (type == "phylogram") {
         phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
-                       horizontal, edge.color, edge.width, edge.lty)
+                       horizontal, edge.color, edge.width)
     } else {
-        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 (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 (root.edge)
       switch(direction,
@@ -333,11 +293,10 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
              "downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge))
     if (show.tip.label) {
         if (!underscore) x$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)
@@ -356,24 +315,36 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
                 adj <- as.numeric(abs(XY$axe) > pi/2)
                 srt <- 180*XY$axe/pi
                 srt[as.logical(adj)] <- srt[as.logical(adj)] - 180
-                ## `srt' takes only a single value, so can't vectorize this:
+                ## <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:
                 for (i in 1:Ntip)
                   text(xx[i], yy[i], cex = cex, x$tip.label[i], adj = adj[i],
                        font = font, srt = srt[i], col = tip.color[i])
             }
         }
         if (type %in% c("fan", "radial")) {
-            xx.tips <- xx[1:Ntip]
-            ## using atan2 considerably facilitates things compared to acos...
-            angle <- atan2(yy[1:Ntip], xx.tips)*180/pi
-            s <- xx.tips < 0
-            angle[s] <- angle[s] + 180
+            xx.scaled <- xx[1:Ntip]
+            if (type == "fan") { # no need if type == "radial"
+                maxx <- max(abs(xx.scaled))
+                if (maxx > 1) xx.scaled <- xx.scaled/maxx
+            }
+            angle <- acos(xx.scaled)*180/pi
+            s1 <- angle > 90 & yy[1:Ntip] > 0
+            s2 <- angle < 90 & yy[1:Ntip] < 0
+            s3 <- angle > 90 & yy[1:Ntip] < 0
+            angle[s1] <- angle[s1] + 180
+            angle[s2] <- -angle[s2]
+            angle[s3] <- 180 - angle[s3]
             adj <- numeric(Ntip)
-            adj[xx.tips < 0] <- 1
-            ## `srt' takes only a single value, so can't vectorize this:
+            adj[xx[1:Ntip] < 0] <- 1
+            ## `srt' takes only a single value, so we cannot vectorize this:
             for (i in 1:Ntip)
-                text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
-                     srt = angle[i], adj = adj[i], col = tip.color[i])
+              text(xx[i], yy[i], x$tip.label[i], font = font, cex = cex,
+                   srt = angle[i], adj = adj[i], col = tip.color[i])
         }
     }
     if (show.node.label)
@@ -391,8 +362,8 @@ 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, edge.lty)
+phylogram.plot <- function(edge, Ntip, Nnode, xx, yy,
+                           horizontal, edge.color, edge.width)
 {
     nodes <- (Ntip + 1):(Ntip + Nnode)
     if (!horizontal) {
@@ -403,134 +374,90 @@ phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
     ## 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) {
-        ii <- i - Ntip
-        j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
-        tmp <- range(yy[edge[j, 2]])
-        y0v[ii] <- tmp[1]
-        y1v[ii] <- tmp[2]
+        j <- edge[which(edge[, 1] == i), 2]
+        y0v[i - Ntip] <- min(yy[j])
+        y1v[i - Ntip] <- max(yy[j])
     }
     ## ... et un trait horizontal partant de chaque tip et chaque noeud
     ##  vers la racine
-    x0h <- xx[edge[, 1]]
-    x1h <- xx[edge[, 2]]
-    y0h <- yy[edge[, 2]]
-
-    nc <- length(edge.color)
-    nw <- length(edge.width)
-    nl <- length(edge.lty)
+    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]]
 
-    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)
-        color.v <- rep("black", Nnode)
+    e.w <- unique(edge.width)
+    if (length(e.w) == 1) width.v <- rep(e.w, Nnode)
+    else {
         width.v <- rep(1, Nnode)
-        lty.v <- rep(1, Nnode)
         for (i in 1:Nnode) {
-            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]
-                }
-            }
+            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 {
+        color.v <- rep("black", 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
         }
     }
 
+    ## we need to reorder `edge.color' and `edge.width':
+    edge.width <- edge.width[pos]
+    edge.color <- edge.color[pos]
     if (horizontal) {
-        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
+        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
     } else {
-        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
+        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
     }
 }
 
-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)
+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)
 
 circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta,
-                          r, edge.color, edge.width, edge.lty)
-### 'edge' must be in pruningwise order
+                          r, edge.color, edge.width)
 {
     r0 <- r[edge[, 1]]
     r1 <- r[edge[, 2]]
     theta0 <- theta[edge[, 2]]
-    costheta0 <- cos(theta0)
-    sintheta0 <- sin(theta0)
 
-    x0 <- r0 * costheta0
-    y0 <- r0 * sintheta0
-    x1 <- r1 * costheta0
-    y1 <- r1 * sintheta0
+    x0 <- r0*cos(theta0)
+    y0 <- r0*sin(theta0)
+    x1 <- r1*cos(theta0)
+    y1 <- r1*sin(theta0)
 
-    segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width, lty = edge.lty)
+    segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width)
 
     tmp <- which(diff(edge[, 1]) != 0)
     start <- c(1, tmp + 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)
+    end <- c(tmp, dim(edge)[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)
-        lines(X*cos(Y), X*sin(Y), col = co[k], lwd = lw[k], lty = ly[k])
+        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)
     }
 }
 
-unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
+unrooted.xy <- function(Ntip, Nnode, edge, edge.length)
 {
     foo <- function(node, ANGLE, AXIS) {
         ind <- which(edge[, 1] == node)
@@ -547,13 +474,19 @@ unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
         for (i in sons)
           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...
-    foo(Ntip + 1L, 2*pi, 0)
+    ## xx[root] <- yy[root] <- 0 # already set!
+    foo(root, 2*pi, 0)
 
     M <- cbind(xx, yy)
     axe <- axis[1:Ntip] # the axis of the terminal branches (for export)