R/plot.phylo.R

In ape: Analyses of Phylogenetics and Evolution

## plot.phylo.R (2022-01-17)

##   Plot Phylogenies

## Copyright 2002-2021 Emmanuel Paradis, 2021 Martin Smith, 2022 Damien de Vienne
## colouring of segments by MS
## tidy trees by DdV

## 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 = NULL, edge.width = NULL, edge.lty = NULL,
             node.color = NULL, node.width = NULL, node.lty = NULL,
             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 = NULL,
             tip.color = par("col"), plot = TRUE, rotate.tree = 0,
             open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)
{
    Ntip <- length(x$tip.label)
    if (Ntip < 2) {
        warning("found fewer than 2 tips in the tree")
        return(NULL)
    }
    .nodeHeight <- function(edge, Nedge, yy)
        .C(node_height, as.integer(edge[, 1]), as.integer(edge[, 2]),
           as.integer(Nedge), as.double(yy))[[4]]

    .nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth)
        .C(node_depth, as.integer(Ntip),
           as.integer(edge[, 1]), as.integer(edge[, 2]),
           as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth))[[5]]

    .nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
        .C(node_depth_edgelength, as.integer(edge[, 1]),
           as.integer(edge[, 2]), as.integer(Nedge),
           as.double(edge.length), double(Ntip + Nnode))[[5]]

    Nedge <- dim(x$edge)[1]
    Nnode <- x$Nnode
    if (any(x$edge < 1) || any(x$edge > Ntip + Nnode))
        stop("tree badly conformed; cannot plot. Check the edge matrix.")
    ROOT <- Ntip + 1
    type <- match.arg(type, c("phylogram", "cladogram", "fan",
                              "unrooted", "radial", "tidy"))
    direction <- match.arg(direction, c("rightwards", "leftwards",
                                        "upwards", "downwards"))
    if (is.null(x$edge.length)) {
        use.edge.length <- FALSE
    } else {
        if (use.edge.length && type != "radial") {
            tmp <- sum(is.na(x$edge.length))
            if (tmp) {
                warning(paste(tmp, "branch length(s) NA(s): branch lengths ignored in the plot"))
                use.edge.length <- FALSE
            }
        }
    }

    if (is.numeric(align.tip.label)) {
        align.tip.label.lty <- align.tip.label
        align.tip.label <- TRUE
    } else { # assumes is.logical(align.tip.labels) == TRUE
        if (align.tip.label) align.tip.label.lty <- 3
    }

    if (align.tip.label) {
        if (type %in% c("unrooted", "radial") || !use.edge.length || is.ultrametric(x))
            align.tip.label <- 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

    phyloORclado <- type %in% c("phylogram", "cladogram", "tidy")
    horizontal <- direction %in% c("rightwards", "leftwards")

    ##tidy exception:
    if (type == "tidy" && any(x$edge.length < 0))
        stop("cannot plot in tidy mode with negative branch lengths. Check 'edge.length' vector.")


    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$edge[, 2], xe[, 2])
                if (length(edge.color) > 1) {
                    edge.color <- rep(edge.color, length.out = Nedge)
                    edge.color <- edge.color[ereorder]
                }
                if (length(edge.width) > 1) {
                    edge.width <- rep(edge.width, length.out = Nedge)
                    edge.width <- edge.width[ereorder]
                }
                if (length(edge.lty) > 1) {
                    edge.lty <- rep(edge.lty, length.out = Nedge)
                    edge.lty <- edge.lty[ereorder]
                }
            }
        }
### By contrats to ape (< 2.4), the arguments edge.color, etc., are
### not elongated before being passed to segments(), except if needed
### to be reordered
        yy <- numeric(Ntip + Nnode)
        TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
        yy[TIPS] <- 1:Ntip
    }

    ## TIDY
    ## Function to compute the size of labels
    ## for each tip in user coordinates
    getStringLengthbyTip <- function(x, lab, sin, cex) {
        s <- strwidth(lab, "inches", cex = cex)
        lim <- getLimit(x, lab, sin, cex)
        alp <- lim/sin
        s*alp
    }
    ### END TIDY

    ## Function to compute the axis limit
    ## x: vector of coordinates, must be positive (or at least the largest value)
    ## lab: vector of labels, length(x) == length(lab)
    ## sin: size of the device in inches
    getLimit <- function(x, lab, sin, cex) {
        s <- strwidth(lab, "inches", cex = cex) # width of the tip labels
        ## if at least one string is larger than the device,
        ## give 1/3 of the plot for the tip labels:
        if (any(s > sin)) return(1.5 * max(x))
        Limit <- 0
        while (any(x > Limit)) {
            i <- which.max(x)
            ## 'alp' is the conversion coeff from inches to user coordinates:
            alp <- x[i]/(sin - s[i])
            Limit <- x[i] + alp*s[i]
            x <- x + alp*s
        }
        Limit
    }
    ## 'z' is the tree in postorder order used in calls to .C
    z <- reorder(x, order = "postorder")

    if (phyloORclado) {
        if (is.null(node.pos))
            node.pos <-
                if (type == "cladogram" && !use.edge.length) 2 else 1

        if (node.pos == 1) {
            yy <- .nodeHeight(z$edge, Nedge, yy)
        } else {
          ## node_height_clado requires the number of descendants
          ## for each node, so we compute `xx' at the same time
          ans <- .C(node_height_clado, as.integer(Ntip),
                    as.integer(z$edge[, 1]), as.integer(z$edge[, 2]),
                    as.integer(Nedge), double(Ntip + Nnode), as.double(yy))
          xx <- ans[[5]] - 1
          yy <- ans[[6]]
        }
        if (!use.edge.length) {
            if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth) - 1
            xx <- max(xx) - xx
        } else  {
            xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
        }
        ## TIDY
        if (type == "tidy") {
            if (!show.tip.label) {
                yy <- tidy.xy(z$edge, Ntip, Nnode, xx, yy)
            } else { # we add to xx the size taken by labels, so that tidying considers labels
                xx.tips <- xx[1:Ntip]
                pin1 <- par("pin")[1] # width of the device in inches
                lab.strlength <- getStringLengthbyTip(xx.tips, x$tip.label, pin1, cex) #size of lab strings
                xx2 <- xx
                xx2[1:Ntip] <- xx2[1:Ntip] + lab.strlength
                yy <- tidy.xy(z$edge, Ntip, Nnode, xx2, yy) #compress taking labels into account
            }
        }
        ### END TIDY
    } else {
        twopi <- 2 * pi
        rotate.tree <- twopi * rotate.tree/360

        if (type != "unrooted") { # for "fan" and "radial" trees (open.angle)
            ## 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]
            xx <- seq(0, twopi * (1 - 1/Ntip) - twopi * open.angle/360,
                      length.out = Ntip)
            theta <- double(Ntip)
            theta[TIPS] <- xx
            theta <- c(theta, numeric(Nnode))
        }

        switch(type, "fan" = {
            theta <- .nodeHeight(z$edge, Nedge, theta)
            if (use.edge.length) {
                r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
            } else {
                r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
                max_r <- max(r)
                r <- (max_r - r + 1) / max_r
            }
            theta <- theta + rotate.tree
            if (root.edge) r <- r + x$root.edge
            xx <- r * cos(theta)
            yy <- r * sin(theta)
        }, "unrooted" = {
            nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
            XY <- if (use.edge.length)
                unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree)
            else
                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$M[, 2])
        }, "radial" = {
            r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
            r[r == 1] <- 0
            r <- 1 - r/Ntip
            theta <- .nodeHeight(z$edge, Nedge, theta) + rotate.tree
            xx <- r * cos(theta)
            yy <- r * sin(theta)
        })
    }

    if (phyloORclado) {
        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 (no.margin) par(mai = rep(0, 4))

    if (show.tip.label) nchar.tip.label <- nchar(x$tip.label)
    max.yy <- max(yy)

    if (is.null(x.lim)) {
        if (phyloORclado) {
            if (horizontal) {
                ## 1.04 comes from that we are using a regular axis system
                ## with 4% on both sides of the range of x:
                ## REMOVED (2017-06-14)
                xx.tips <- xx[1:Ntip]# * 1.04
                if (show.tip.label) {
                    pin1 <- par("pin")[1] # width of the device in inches
                    tmp <- getLimit(xx.tips, x$tip.label, pin1, cex)
                    tmp <- tmp + label.offset
                } else tmp <- max(xx.tips)
                x.lim <- c(0, tmp)
            } else {
                ### TIDY
                ## x.lim <- c(1, Ntip) # Not true anymore with tidy trees
                x.lim <- c(1, max(xx[1:Ntip])) # add offset?
                ### END TIDY
            }
        } else switch(type, "fan" = {
            if (show.tip.label) {
                offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
                x.lim <- range(xx) + c(-offset, offset)
            } else x.lim <- range(xx)
        }, "unrooted" = {
            if (show.tip.label) {
                offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
                x.lim <- c(0 - offset, max(xx) + offset)
            } else x.lim <- c(0, max(xx))
        }, "radial" = {
            if (show.tip.label) {
                offset <- max(nchar.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
        if (type %in% c("fan", "unrooted") && show.tip.label)
            x.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy * cex)
        if (type == "radial")
            x.lim[1] <-
                if (show.tip.label) -1 - max(nchar.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) {
                ### TIDY
                ## y.lim <- c(1, Ntip) # Not true anymore with tidy trees
                y.lim <- c(1, max(yy[1:Ntip]))
                ### END TIDY
            } else {
                pin2 <- par("pin")[2] # height of the device in inches
                ## 1.04 comes from that we are using a regular axis system
                ## with 4% on both sides of the range of x:
                ## REMOVED (2017-06-14)
                yy.tips <- yy[1:Ntip]# * 1.04
                if (show.tip.label) {
                    tmp <- getLimit(yy.tips, x$tip.label, pin2, cex)
                    tmp <- tmp + label.offset
                } else tmp <- max(yy.tips)
                y.lim <- c(0, tmp)
            }
        } else switch(type, "fan" = {
            if (show.tip.label) {
                offset <- max(nchar.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 (show.tip.label) {
                offset <- max(nchar.tip.label * 0.018 * max.yy * cex)
                y.lim <- c(0 - offset, max.yy + offset)
            } else y.lim <- c(0, max.yy)
        }, "radial" = {
            if (show.tip.label) {
                offset <- max(nchar.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.tip.label * 0.018 * max.yy * cex)
        if (type == "radial")
            y.lim[1] <- if (show.tip.label) -1 - max(nchar.tip.label * 0.018 * max.yy * cex) else -1
    }
    ## mirror the yy:
    if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy # fix by Klaus
    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.default(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
                 ylab = "", axes = FALSE, asp = asp, ...)

    if (plot) {
        if (is.null(adj))
            adj <- if (phyloORclado && direction == "leftwards") 1 else 0
        if (phyloORclado && show.tip.label) {
            MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
            loy <- 0
            if (direction == "rightwards") {
                lox <- label.offset + MAXSTRING * 1.05 * adj
            }
            if (direction == "leftwards") {
                lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
                ##xx <- xx + MAXSTRING
            }
            if (!horizontal) {
                psr <- par("usr")
                MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
                loy <- label.offset + MAXSTRING * 1.05 * adj
                lox <- 0
                srt <- 90 + srt
                if (direction == "downwards") {
                    loy <- -loy
                    ##yy <- yy + MAXSTRING
                    srt <- 180 + srt
                }
            }
        }
        if (type %in% c("phylogram", "tidy")) {
            phylogram.plot(x$edge, Ntip, Nnode, xx, yy, horizontal,
                           edge.color, edge.width, edge.lty,
                           node.color, node.width, node.lty)
        } else {
            if (is.null(edge.color)) {
                edge.color <- par('fg')
            }
            if (is.null(edge.width)) {
                edge.width <- par('lwd')
            }
            if (is.null(edge.lty)) {
                edge.lty <- par('lty')
            }

            if (type == "fan") {
                ereorder <- match(z$edge[, 2], x$edge[, 2])
                if (length(edge.color) > 1) {
                    edge.color <- rep_len(edge.color, Nedge)
                    edge.color <- edge.color[ereorder]
                }
                if (length(edge.width) > 1) {
                    edge.width <- rep_len(edge.width, Nedge)
                    edge.width <- edge.width[ereorder]
                }
                if (length(edge.lty) > 1) {
                    edge.lty <- rep_len(edge.lty, 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) {
            rootcol <- if (length(edge.color) == 1) edge.color else par("fg")
            rootw <- if (length(edge.width) == 1) edge.width else par("lwd")
            rootlty <- if (length(edge.lty) == 1) edge.lty else par("lty")
            if (type == "fan") {
                tmp <- polar2rect(x$root.edge, theta[ROOT])
                segments(0, 0, tmp$x, tmp$y, col = rootcol, lwd = rootw, lty = rootlty)
            } else {
                switch(direction,
                       "rightwards" = segments(0, yy[ROOT], x$root.edge, yy[ROOT],
                                               col = rootcol, lwd = rootw, lty = rootlty),
                       "leftwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT],
                                              col = rootcol, lwd = rootw, lty = rootlty),
                       "upwards" = segments(xx[ROOT], 0, xx[ROOT], x$root.edge,
                                            col = rootcol, lwd = rootw, lty = rootlty),
                       "downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge,
                                              col = rootcol, lwd = rootw, lty = rootlty))
            }
        }
        if (show.tip.label) {
            if (is.expression(x$tip.label)) underscore <- TRUE
            if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)

            if (phyloORclado) {
                if (align.tip.label) {
                    xx.tmp <- switch(direction,
                                     "rightwards" = max(xx[1:Ntip]),
                                     "leftwards" = min(xx[1:Ntip]),
                                     "upwards" = xx[1:Ntip],
                                     "downwards" = xx[1:Ntip])
                    yy.tmp <- switch(direction,
                                     "rightwards" = yy[1:Ntip],
                                     "leftwards" = yy[1:Ntip],
                                     "upwards" = max(yy[1:Ntip]),
                                     "downwards" = min(yy[1:Ntip]))
                    segments(xx[1:Ntip], yy[1:Ntip], xx.tmp, yy.tmp, lty = align.tip.label.lty)
                } else {
                    xx.tmp <- xx[1:Ntip]
                    yy.tmp <- yy[1:Ntip]
                }
                text(xx.tmp + lox, yy.tmp + loy, x$tip.label, adj = adj,
                     font = font, srt = srt, cex = cex, col = tip.color)
            } else {
                angle <- if (type == "unrooted") XY$axe else atan2(yy[1:Ntip], xx[1:Ntip]) # in radians

                lab4ut <-
                    if (is.null(lab4ut)) {
                        if (type == "unrooted") "horizontal" else "axial"
                    } else match.arg(lab4ut, c("horizontal", "axial"))

                xx.tips <- xx[1:Ntip]
                yy.tips <- yy[1:Ntip]
                if (label.offset) {
                    xx.tips <- xx.tips + label.offset * cos(angle)
                    yy.tips <- yy.tips + label.offset * sin(angle)
                }

                if (lab4ut == "horizontal") {
                    y.adj <- x.adj <- numeric(Ntip)
                    sel <- abs(angle) > 0.75 * pi
                    x.adj[sel] <- -strwidth(x$tip.label)[sel] * 1.05
                    sel <- abs(angle) > pi/4 & abs(angle) < 0.75 * pi
                    x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(angle)[sel] / pi - 0.5)
                    sel <- angle > pi / 4 & angle < 0.75 * pi
                    y.adj[sel] <- strheight(x$tip.label)[sel] / 2
                    sel <- angle < -pi / 4 & angle > -0.75 * pi
                    y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
                    text(xx.tips + x.adj * cex, yy.tips + y.adj * cex,
                         x$tip.label, adj = c(adj, 0), font = font,
                         srt = srt, cex = cex, col = tip.color)
                } else { # if lab4ut == "axial"
                    if (align.tip.label) {
                        POL <- rect2polar(xx.tips, yy.tips)
                        POL$r[] <- max(POL$r)
                        REC <- polar2rect(POL$r, POL$angle)
                        xx.tips <- REC$x
                        yy.tips <- REC$y
                        segments(xx[1:Ntip], yy[1:Ntip], xx.tips, yy.tips, lty = align.tip.label.lty)
                    }
                    if (type == "unrooted") {
                        adj <- abs(angle) > pi/2
                        angle <- angle * 180/pi # switch to degrees
                        angle[adj] <- angle[adj] - 180
                        adj <- as.numeric(adj)
                    } else {
                        s <- xx.tips < 0
                        angle <- angle * 180/pi
                        angle[s] <- angle[s] + 180
                        adj <- as.numeric(s)
                    }
                    ## `srt' takes only a single value, so can't vectorize this:
                    ## (and need to 'elongate' these vectors:)
                    font <- rep(font, length.out = Ntip)
                    tip.color <- rep(tip.color, length.out = Ntip)
                    cex <- rep(cex, length.out = Ntip)
                    for (i in 1:Ntip)
                        text(xx.tips[i], yy.tips[i], x$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$node.label, adj = adj, font = font, srt = srt, cex = cex)
    }
    L <- list(type = type, use.edge.length = use.edge.length,
              node.pos = node.pos, node.depth = node.depth,
              show.tip.label = show.tip.label,
              show.node.label = show.node.label, font = font,
              cex = cex, adj = adj, srt = srt, no.margin = no.margin,
              label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
              direction = direction, tip.color = tip.color,
              Ntip = Ntip, Nnode = Nnode, root.time = x$root.time,
              align.tip.label = align.tip.label)
    assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
           envir = .PlotPhyloEnv)
    invisible(L)
}

phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
                           edge.color = NULL, edge.width = NULL,
                           edge.lty = NULL,
                           node.color = NULL, node.width = NULL,
                           node.lty = NULL)
{
    nodes <- Ntip + seq_len(Nnode)
    if (!horizontal) {
        tmp <- yy
        yy <- xx
        xx <- tmp
    }
    ## un trait vertical a chaque noeud...
    x0v <- xx[nodes]
    y0v <- y1v <- numeric(Nnode)

    e1 <- edge[, 1]
    e2 <- edge[, 2]
    Nedge <- length(e1)

    ## store the index of each node in the 1st column of edge:
    NodeInEdge1 <- lapply(Ntip + seq_len(Nnode), function (j) which(e1 == j))
    edgeChildren <- lapply(NodeInEdge1, function (nie) e2[nie])
    yv <- vapply(edgeChildren, function (i) range(yy[i]), double(2))
    y0v <- yv[1, ]
    y1v <- yv[2, ]

    ## ... et un trait horizontal partant de chaque tip et chaque noeud
    ##  vers la racine
    x0h <- xx[e1]
    x1h <- xx[e2]
    y0h <- yy[e2]

    # Node and edge styling

    .one.style <- function (style) {
        list(h = rep_len(style, Nedge), v = rep_len(style, Ntip + Nnode))
    }

    .edge.style <- function (node.style) {
        node.style <- rep_len(node.style, Ntip + Nnode)
        sapply(seq_len(Nedge), function (e) node.style[e2[e]])
    }

    .node.style <- function (edge.style, fallback) {
        edge.style <- rep_len(edge.style, Nedge)
        c(character(Ntip),
          sapply(Ntip + seq_len(Nnode), function (n) {
              pendant.styles <- edge.style[e1 == n]
              if (length(unique(pendant.styles)) == 1L) {
                  pendant.styles[1]
              } else {
                  fallback
              }
          }))
    }

    .style <- function (edge.style, node.style, stylePar) {
        if (missing(edge.style) || is.null(edge.style)) {
            if (missing(node.style) || is.null(node.style)) {
                return(.one.style(par(stylePar)))
            } else {
                if (length(node.style) == 1L) {
                    return(.one.style(node.style))
                } else {
                    return(list(h = .edge.style(node.style),
                                v = rep_len(node.style, Ntip + Nnode)))
                }
            }
        } else if (missing(node.style) || is.null(node.style)) {
            if (length(edge.style) == 1L) {
                return(.one.style(edge.style))
            } else {
                return(list(h = rep_len(edge.style, Nedge),
                            v = .node.style(edge.style, par(stylePar))))
            }
        } else {

            return(list(h = rep_len(edge.style, Nedge),
                        v = rep_len(node.style, Ntip + Nnode)))
        }
    }

    .LtyToStr <- function (x) {
        if (is.numeric(x)) {
            c("blank", "solid", "dashed", "dotted", "dotdash", "longdash",
              "twodash")[x + 1L]
        } else {
            x
        }
    }

    colors <- .style(edge.color, node.color, 'fg')
    widths <- .style(edge.width, node.width, 'lwd')
    ltys <- .style(.LtyToStr(edge.lty), .LtyToStr(node.lty), 'lty')

    edge.color <- colors$h
    edge.width <- widths$h
    edge.lty <- ltys$h

    color.v <- colors$v[-seq_len(Ntip)]
    width.v <- widths$v[-seq_len(Ntip)]
    lty.v <- ltys$v[-seq_len(Ntip)]

    DF <- data.frame(edge.color, edge.width, edge.lty, stringsAsFactors = FALSE)
    DF <- DF[, c(is.null(node.color), is.null(node.width), is.null(node.lty)),
             drop = FALSE]

    for (i in seq_len(Nnode)) {
        br <- NodeInEdge1[[i]]
        if (length(br) == 2) {
            A <- br[1]
            B <- br[2]

            # We should draw a single line if at all possible, for the
            # appearance of dotted / dashed line styles.
            if (any(DF[A, ] != DF[B, ])) {
                ## add a new line:
                y0v <- c(y0v, y0v[i])
                y1v <- c(y1v, yy[i + Ntip])
                x0v <- c(x0v, x0v[i])
                ## shorten the old line:
                y0v[i] <- yy[i + Ntip]

                if (is.null(node.color)) {
                    # Half-lines may have different colours
                    color.v[i] <- edge.color[B]
                    color.v <- c(color.v, edge.color[A])
                } else {
                    # Use node colour for both half-lines
                    color.v <- c(color.v, color.v[i])
                }
                if (is.null(node.width)) {
                    width.v[i] <- edge.width[B]
                    width.v <- c(width.v, edge.width[A])
                } else {
                    width.v <- c(width.v, width.v[i])
                }
                if (is.null(node.lty)) {
                    lty.v[i] <- edge.lty[B]
                    lty.v <- c(lty.v, edge.lty[A])
                } else {
                    lty.v <- c(lty.v, lty.v[i])
                }
            }
        }
    }

    if (horizontal) {
        # draw horizontal lines
        segments(x0h, y0h, x1h, y0h,
                 col = edge.color, lwd = edge.width, lty = edge.lty)
        # draw vertical lines
        segments(x0v, y0v, x0v, y1v,
                 col = color.v, lwd = width.v, lty = lty.v)
    } else {
        # draws vertical lines
        segments(y0h, x0h, y0h, x1h,
                 col = edge.color, lwd = edge.width, lty = edge.lty)
        # draws horizontal lines
        segments(y0v, x0v, y1v, x0v,
                 col = color.v, lwd = width.v, lty = lty.v)
    }
}

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, edge.lty)
### 'edge' must be in postorder order
{
    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

    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)
    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(as.list(rep(edge.feat, Nnode)))
        edge.feat <- rep(edge.feat, length.out = Nedge)
        feat.arc <- as.list(rep(default, Nnode))
        for (k in 1:Nnode) {
            tmp <- edge.feat[start[k]]
            if (tmp == edge.feat[end[k]]) { # fix by Francois Michonneau (2015-07-24)
                feat.arc[[k]] <- tmp
            } else {
                if (nodedegree[k] == 2)
                    feat.arc[[k]] <- rep(c(tmp, edge.feat[end[k]]), each = 50)
            }
        }
        feat.arc
    }
    nodedegree <- tabulate(edge[, 1L])[-seq_len(Ntip)]
    co <- foo(edge.color, par("fg"))
    lw <- foo(edge.width, par("lwd"))
    ly <- foo(edge.lty, par("lty"))

    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)
        x <- X * cos(Y); y <- X * sin(Y)
        x0 <- x[-100]; y0 <- y[-100]; x1 <- x[-1]; y1 <- y[-1]
        segments(x0, y0, x1, y1, col = co[[k]], lwd = lw[[k]], lty = ly[[k]])
    }
}

unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree)
{
    foo <- function(node, ANGLE, AXIS) {
        ind <- which(edge[, 1] == node)
        sons <- edge[ind, 2]
        start <- AXIS - ANGLE/2
        for (i in 1:length(sons)) {
            h <- edge.length[ind[i]]
            angle[sons[i]] <<- alpha <- ANGLE*nb.sp[sons[i]]/nb.sp[node]
            axis[sons[i]] <<- beta <- start + alpha/2
            start <- start + alpha
            xx[sons[i]] <<- h*cos(beta) + xx[node]
            yy[sons[i]] <<- h*sin(beta) + yy[node]
        }
        for (i in sons)
            if (i > Ntip) foo(i, angle[i], axis[i])
    }
    Nedge <- dim(edge)[1]
    yy <- xx <- numeric(Ntip + Nnode)
    ## `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 + rotate.tree)

    M <- cbind(xx, yy)
    axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
    axeGTpi <- axe > pi
    ## make sure that the returned angles are in [-PI, +PI]:
    axe[axeGTpi] <- axe[axeGTpi] - 2*pi
    list(M = M, axe = axe)
}

node.depth <- function(phy, method = 1)
{
    n <- length(phy$tip.label)
    m <- phy$Nnode
    N <- dim(phy$edge)[1]
    phy <- reorder(phy, order = "postorder")
    .C(node_depth, as.integer(n),
       as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
       as.integer(N), double(n + m), as.integer(method))[[5]]
}

node.depth.edgelength <- function(phy)
{
    n <- length(phy$tip.label)
    m <- phy$Nnode
    N <- dim(phy$edge)[1]
    phy <- reorder(phy, order = "postorder")
    .C(node_depth_edgelength, as.integer(phy$edge[, 1]),
       as.integer(phy$edge[, 2]), as.integer(N),
       as.double(phy$edge.length), double(n + m))[[5]]
}

node.height <- function(phy, clado.style = FALSE)
{
    n <- length(phy$tip.label)
    m <- phy$Nnode
    N <- dim(phy$edge)[1]

    phy <- reorder(phy)
    yy <- numeric(n + m)
    e2 <- phy$edge[, 2]
    yy[e2[e2 <= n]] <- 1:n

    phy <- reorder(phy, order = "postorder")
    e1 <- phy$edge[, 1]
    e2 <- phy$edge[, 2]

    if (clado.style)
        .C(node_height_clado, as.integer(n), as.integer(e1),
           as.integer(e2), as.integer(N), double(n + m), as.double(yy))[[6]]
    else
        .C(node_height, as.integer(e1), as.integer(e2), as.integer(N),
           as.double(yy))[[4]]
}

plot.multiPhylo <- function(x, layout = 1, ...)
{
    layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
    if (!devAskNewPage() && names(dev.cur()) %in% deviceIsInteractive()) {
        devAskNewPage(TRUE)
        on.exit(devAskNewPage(FALSE))
    }
    for (i in seq_along(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 && !devAskNewPage() && interactive()) {
        devAskNewPage(TRUE)
        on.exit(devAskNewPage(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 ;)
}

### TIDY
tidy.xy <- function(edge, Ntip, Nnode, xx, yy)
{
    yynew <- yy # will be updated to get the new y coordinates after tidying
    ## initialrange<-diff(range(yy)) #for computing compression. Remove ?

    oedge <- edge[match(seq_len(Ntip + Nnode), edge[, 2]), 1] # ordered edges
    segofnodes <- data.frame(x1 = xx[oedge], y1 = yy, x2 = xx, y2 = yy) # segment associated to each node

    postordernodes <- edge[,2]
    nodes <- c(postordernodes[order(xx[postordernodes], decreasing = TRUE)], Ntip + 1) # ensures equal x values to not lead to erroneuos postoder of nodes

    GetContourPairsFromSegments <- function(seg, which) {
        if (nrow(seg) > 1) { #solves issue with branch length = 0
            allx <- sort(unique(c(seg$x1, seg$x2)))
            newx2 <- allx[2:length(allx)]
            if (which == "top") {
                newy2i <- sapply(newx2, function(cx, se) which(cx > se$x1 & cx <= se$x2)[which.max(se$y1[which(cx > se$x1 & cx <= se$x2)])], se = seg)
            }
            if (which == "bottom") {
                newy2i <- sapply(newx2, function(cx, se) which(cx > se$x1 & cx <= se$x2)[which.min(se$y1[which(cx > se$x1 & cx <= se$x2)])], se = seg)
            }

            newx1 <- allx[1:(length(allx) - 1)]
            newy1i <- newy2i
            ## we simplify segments by merging thsoe on same horiz  (bout a bout)
            where2mergei <- which((newy1i[2:length(newy1i)] - newy2i[1:(length(newy1i) - 1)]) == 0)
            if (length(where2mergei) > 0) {
                newx1 <- newx1[-(where2mergei + 1)]
                newy1i <- newy1i[-(where2mergei + 1)]
                newx2 <- newx2[-(where2mergei)]
                newy2i <- newy2i[-(where2mergei)]
            }

            newy1ok <- seg$y1[newy1i]
            newy2ok <- newy1ok
            newseg <- data.frame(x1 = newx1, y1 = newy1ok, x2 = newx2, y2 = newy2ok)
        } else {
            newseg <- seg
        }
        newseg
    }
    GetMinDistBetweenContours <- function(topcontour, bottomcontour) {
        ## efficient way to compare top and bottom contour by only looking
        ## at necessary pairs (see original publiction)
        d <- NULL
        topi <- 1
        boti <- 1
        while((topi <= nrow(topcontour)) & (boti <= nrow(bottomcontour))) {
            d <- c(d, bottomcontour[boti, ]$y1 - topcontour[topi, ]$y1)
            if (bottomcontour[boti, ]$x2 < topcontour[topi, ]$x2) boti <- boti + 1
            else topi <- topi + 1
        }
        min(d)
    }

    N <- list() # will contain all info for each node.
    for (n in nodes) {
        N[[n]] <- list()
        childs <- edge[edge[, 1] == n, 2]
        childs.ord <- childs[order(yy[childs])] # childs ordered by y values
        desc <- c(childs, unlist(lapply(N[childs], function(x) x$desc)))

        diffiny <- 0

        if (n > Ntip) { # we are in a node
            oldyofcurrentnode <- yynew[n]
            for (nn in 2:length(childs.ord)) {
                top <- N[[childs.ord[nn - 1]]]$segtop
                bot <- N[[childs.ord[nn]]]$segbottom
                mindist <- GetMinDistBetweenContours(top, bot)
                if (mindist != 1) { # There is room for tidying or untidy up if branches are tangled
                    mod <- mindist - 1
                    N[[childs.ord[nn]]]$segbottom[, c(2, 4)] <- N[[childs.ord[nn]]]$segbottom[, c(2, 4)] - mod
                    N[[childs.ord[nn]]]$segtop[, c(2, 4)] <- N[[childs.ord[nn]]]$segtop[, c(2, 4)] - mod

                    yynew[c(childs.ord[nn], N[[childs.ord[nn]]]$desc)] <- yynew[c(childs.ord[nn], N[[childs.ord[nn]]]$desc)] - mod
                }
            }
            newyofcurrentnode <- mean(range(yynew[childs.ord]))
            yynew[n] <- newyofcurrentnode
            diffiny <- oldyofcurrentnode - newyofcurrentnode
        }

        descseg <- segofnodes[n, ]
        descseg[, c(2, 4)] <- descseg[, c(2, 4)] - diffiny
        segtop.pre <- rbind(descseg, do.call(rbind, lapply(N[childs], function(x) x$segtop)))
        segtop <- GetContourPairsFromSegments(segtop.pre, "top")
        segbottom.pre <- rbind(descseg, do.call(rbind, lapply(N[childs], function(x) x$segbottom)))
        segbottom <- GetContourPairsFromSegments(segbottom.pre, "bottom")

        N[[n]]$childs <- childs.ord
        N[[n]]$desc <- desc
        N[[n]]$segtop <- segtop
        N[[n]]$segbottom <- segbottom
    }
    yynew <- yynew - (min(yynew) - 1) ## so that min(y)=1 always
    ## finalrange <- diff(range(yynew)) #for computing compression. Remove?
    ## compression <- ((initialrange-finalrange)/initialrange)*100 # Remove?
    ## print(paste("Compression: ", round(compression,2),"%", sep="")) #Remove?
    yynew
}

### END TIDY