R/plot.phylo.R

Defines functions kronoviz trex plot.multiPhylo node.height node.depth.edgelength node.depth unrooted.xy circular.plot cladogram.plot phylogram.plot plot.phylo

Documented in circular.plot cladogram.plot kronoviz node.depth node.depth.edgelength node.height phylogram.plot plot.multiPhylo plot.phylo trex unrooted.xy

## plot.phylo.R (2016-07-01)

##   Plot Phylogenies

## Copyright 2002-2016 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, 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 = NULL,
             tip.color = "black", plot = TRUE, rotate.tree = 0,
             open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)
{
    Ntip <- length(x$tip.label)
    if (Ntip < 2) {
        warning("found less than 2 tips in the tree")
        return(NULL)
    }
    if (any(tabulate(x$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))[[6]]

    .nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth)
        .C(node_depth, as.integer(Ntip), as.integer(Nnode),
           as.integer(edge[, 1]), as.integer(edge[, 2]),
           as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth))[[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))[[7]]

    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"))
    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")
    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$edge[, 2], xe[, 2])
                if (length(edge.color) > 1) {
                    edge.color <- rep(edge.color, length.out = Nedge)
                    edge.color <- edge.color[ereorder]
                }
                if (length(edge.width) > 1) {
                    edge.width <- rep(edge.width, length.out = Nedge)
                    edge.width <- edge.width[ereorder]
                }
                if (length(edge.lty) > 1) {
                    edge.lty <- rep(edge.lty, length.out = Nedge)
                    edge.lty <- edge.lty[ereorder]
                }
            }
        }
### By contrats to ape (< 2.4), the arguments edge.color, etc., are
### not elongated before being passed to segments(), except if needed
### to be reordered
        yy <- numeric(Ntip + Nnode)
        TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
        yy[TIPS] <- 1:Ntip
    }
    ## '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(Ntip, Nnode, z$edge, Nedge, yy)
        else {
          ## node_height_clado requires the number of descendants
          ## for each node, so we compute `xx' at the same time
          ans <- .C(node_height_clado, as.integer(Ntip),
                    as.integer(Nnode), as.integer(z$edge[, 1]),
                    as.integer(z$edge[, 2]), as.integer(Nedge),
                    double(Ntip + Nnode), as.double(yy))
          xx <- ans[[6]] - 1
          yy <- ans[[7]]
        }
        if (!use.edge.length) {
            if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth) - 1
            xx <- max(xx) - xx
        } else  {
            xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
        }
} 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(Ntip, Nnode, 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)
            r <- 1/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(Ntip, Nnode, 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) {
                x.lim <- c(0, NA)
                pin1 <- par("pin")[1] # width of the device in inches
                strWi <- strwidth(x$tip.label, "inches", cex = cex) # id. for the tip labels
                ## 1.04 comes from that we are using a regular axis system
                ## with 4% on both sides of the range of x:
                xx.tips <- xx[1:Ntip] * 1.04
                ## 'alp' is the conversion coefficient from
                ## user coordinates to inches:
                alp <- try(uniroot(function(a) max(a*xx.tips + strWi) - pin1,
                                   c(0, 1e6))$root, silent = TRUE)
                ## if the above fails, give 1/3 of the plot for the tip labels:
                if (is.character(alp)) {
                    tmp <- max(xx.tips)
                    if (show.tip.label) tmp <- tmp * 1.5 # fix by Liam Revell (2015-06-22)
                } else {
                    tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
                }
                if (show.tip.label) tmp <- tmp + label.offset
                x.lim[2] <- tmp
            } else x.lim <- c(1, Ntip)
        } 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) y.lim <- c(1, Ntip) else {
                y.lim <- c(0, NA)
                pin2 <- par("pin")[2] # height of the device in inches
                strWi <- strwidth(x$tip.label, "inches", cex = cex)
                ## 1.04 comes from that we are using a regular axis system
                ## with 4% on both sides of the range of x:
                yy.tips <- yy[1:Ntip] * 1.04
                ## 'alp' is the conversion coefficient from
                ## user coordinates to inches:
                alp <- try(uniroot(function(a) max(a*yy.tips + strWi) - pin2,
                                   c(0, 1e6))$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)
                    if (show.tip.label) tmp <- tmp * 1.5
                } else {
                    tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
                }
                if (show.tip.label) tmp <- tmp + label.offset
                y.lim[2] <- 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$tip.label, cex = cex))
        loy <- 0
        if (direction == "rightwards") {
            lox <- label.offset + MAXSTRING * 1.05 * adj
        }
        if (direction == "leftwards") {
            lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
            ##xx <- xx + MAXSTRING
        }
        if (!horizontal) {
            psr <- par("usr")
            MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
            loy <- label.offset + MAXSTRING * 1.05 * adj
            lox <- 0
            srt <- 90 + srt
            if (direction == "downwards") {
                loy <- -loy
                ##yy <- yy + MAXSTRING
                srt <- 180 + srt
            }
        }
    }
    if (type == "phylogram") {
        phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
                       horizontal, edge.color, edge.width, edge.lty)
    } 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 (root.edge) {
        rootcol <- if (length(edge.color) == 1) edge.color else "black"
        rootw <- if (length(edge.width) == 1) edge.width else 1
        rootlty <- if (length(edge.lty) == 1) edge.lty else 1
        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, edge.width, edge.lty)
{
    nodes <- (Ntip + 1):(Ntip + Nnode)
    if (!horizontal) {
        tmp <- yy
        yy <- xx
        xx <- tmp
    }
    ## un trait vertical a 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)
    e1 <- edge[, 1]
    for (i in seq_along(e1)) {
        j <- e1[i] - Ntip
        NodeInEdge1[[j]] <- c(NodeInEdge1[[j]], i)
    }

    for (i in 1:Nnode) {
        j <- NodeInEdge1[[i]]
        tmp <- range(yy[edge[j, 2]])
        y0v[i] <- tmp[1]
        y1v[i] <- tmp[2]
    }
    ## ... 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)

    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 <- 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]
                }
            }
        }
    }

    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
    } 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
    }
}

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, "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)
        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
    ## insures that 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$edge)[1]
    phy <- reorder(phy, order = "postorder")
    .C(node_depth, as.integer(n), as.integer(m),
       as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
       as.integer(N), double(n + m), as.integer(method))[[6]]
}

node.depth.edgelength <- function(phy)
{
    n <- length(phy$tip.label)
    m <- phy$Nnode
    N <- dim(phy$edge)[1]
    phy <- reorder(phy, order = "postorder")
    .C(node_depth_edgelength, as.integer(n), as.integer(n),
       as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
       as.integer(N), as.double(phy$edge.length), double(n + m))[[7]]
}

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(m),
           as.integer(e1), as.integer(e2), as.integer(N),
           double(n + m), as.double(yy))[[7]]
    else
        .C(node_height, as.integer(n), as.integer(m),
           as.integer(e1), as.integer(e2), as.integer(N),
           as.double(yy))[[6]]
}

plot.multiPhylo <- function(x, layout = 1, ...)
{
    layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
    if (!devAskNewPage() && !names(dev.cur()) %in% c("pdf", "postscript")) {
        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 ;)
}

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ape documentation built on May 30, 2017, 6:11 a.m.