X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fplot.phylo.R;h=96d9aa4e590a6f4b9262335d480fc197ea950076;hb=a0436318d70829a2d16134be7ca1d6d454613a20;hp=18bba88509dd0bab1e37b91d3b274c26a6aee316;hpb=3f91879755fdbbe39cfd936495b2985fa4621615;p=ape.git diff --git a/R/plot.phylo.R b/R/plot.phylo.R index 18bba88..96d9aa4 100644 --- a/R/plot.phylo.R +++ b/R/plot.phylo.R @@ -1,24 +1,26 @@ -## plot.phylo.R (2011-03-23) +## plot.phylo.R (2012-12-19) ## Plot Phylogenies -## Copyright 2002-2011 Emmanuel Paradis +## Copyright 2002-2012 Emmanuel Paradis ## This file is part of the R-package `ape'. ## See the file ../COPYING for licensing issues. -plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, - node.pos = NULL, show.tip.label = TRUE, - show.node.label = FALSE, edge.color = "black", - edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), - adj = NULL, srt = 0, no.margin = FALSE, - root.edge = FALSE, label.offset = 0, underscore = FALSE, - x.lim = NULL, y.lim = NULL, direction = "rightwards", - lab4ut = "horizontal", tip.color = "black", ...) +plot.phylo <- + function(x, type = "phylogram", use.edge.length = TRUE, + node.pos = NULL, show.tip.label = TRUE, + show.node.label = FALSE, edge.color = "black", + edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), + adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE, + label.offset = 0, underscore = FALSE, x.lim = NULL, + y.lim = NULL, direction = "rightwards", lab4ut = "horizontal", + tip.color = "black", plot = TRUE, rotate.tree = 0, + open.angle = 0, ...) { Ntip <- length(x$tip.label) - if (Ntip == 1) { - warning("found only one tip in the tree") + if (Ntip < 2) { + warning("found less than 2 tips in the tree") return(NULL) } if (any(tabulate(x$edge[, 1]) == 1)) @@ -95,17 +97,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, } ## '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 + if (phyloORclado) { if (is.null(node.pos)) { node.pos <- 1 @@ -130,12 +122,16 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, } else { xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length) } - } else switch(type, "fan" = { + } else { + twopi <- 2 * pi + rotate.tree <- twopi * rotate.tree/360 + switch(type, "fan" = { ## if the tips are not in the same order in tip.label ## and in edge[, 2], we must reorder the angles: we ## use `xx' to store temporarily the angles TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2] - xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip) + 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)) @@ -146,14 +142,15 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) r <- 1/r } - xx <- r*cos(theta) - yy <- r*sin(theta) + theta <- theta + rotate.tree + xx <- r * cos(theta) + yy <- r * sin(theta) }, "unrooted" = { nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) XY <- if (use.edge.length) - unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp) + unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp, rotate.tree) else - unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp) + unrooted.xy(Ntip, Nnode, z$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]) @@ -163,11 +160,11 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, ## radius: X <- 1 - X/Ntip ## angle (1st compute the angles for the tips): - yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode)) + yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode)) Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy) - xx <- X * cos(Y) - yy <- X * sin(Y) - }) + xx <- X * cos(Y + rotate.tree) + yy <- X * sin(Y + rotate.tree) + })} if (phyloORclado) { if (!horizontal) { tmp <- yy @@ -266,18 +263,20 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, y.lim <- c(0, y.lim) if (phyloORclado && horizontal) y.lim[1] <- 1 if (type %in% c("fan", "unrooted") && show.tip.label) - y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex) + y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex) if (type == "radial") - y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1 + y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1 } ## mirror the yy: - if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy + if (phyloORclado && direction == "downwards") yy <- max(yy) - yy if (phyloORclado && root.edge) { if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge } asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12) plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...) + +if (plot) { if (is.null(adj)) adj <- if (phyloORclado && direction == "leftwards") 1 else 0 if (phyloORclado && show.tip.label) { @@ -288,7 +287,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, } if (direction == "leftwards") { lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj) - #xx <- xx + MAXSTRING + ##xx <- xx + MAXSTRING } if (!horizontal) { psr <- par("usr") @@ -379,7 +378,6 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, if (type %in% c("fan", "radial")) { xx.tips <- xx[1:Ntip] yy.tips <- yy[1:Ntip] - ## using atan2 considerably facilitates things compared to acos... angle <- atan2(yy.tips, xx.tips) # in radians if (label.offset) { xx.tips <- xx.tips + label.offset * cos(angle) @@ -403,6 +401,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE, if (show.node.label) text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)], x$node.label, adj = adj, font = font, srt = srt, cex = cex) +} L <- list(type = type, use.edge.length = use.edge.length, node.pos = node.pos, show.tip.label = show.tip.label, show.node.label = show.node.label, font = font, @@ -424,7 +423,7 @@ phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal, yy <- xx xx <- tmp } - ## un trait vertical à chaque noeud... + ## 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: @@ -554,7 +553,7 @@ circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta, } } -unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp) +unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) { foo <- function(node, ANGLE, AXIS) { ind <- which(edge[, 1] == node) @@ -569,7 +568,7 @@ unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp) yy[sons[i]] <<- h*sin(beta) + yy[node] } for (i in sons) - if (i > Ntip) foo(i, angle[i], axis[i]) + if (i > Ntip) foo(i, angle[i], axis[i]) } Nedge <- dim(edge)[1] yy <- xx <- numeric(Ntip + Nnode) @@ -577,7 +576,7 @@ unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp) ## `axis': the axis of each branch axis <- angle <- numeric(Ntip + Nnode) ## start with the root... - foo(Ntip + 1L, 2*pi, 0) + foo(Ntip + 1L, 2*pi, 0 + rotate.tree) M <- cbind(xx, yy) axe <- axis[1:Ntip] # the axis of the terminal branches (for export) @@ -598,6 +597,57 @@ node.depth <- function(phy) as.integer(N), double(n + m), DUP = FALSE, PACKAGE = "ape")[[6]] } +node.depth.edgelength <- function(phy) +{ + n <- length(phy$tip.label) + m <- phy$Nnode + N <- dim(phy$edge)[1] + phy <- reorder(phy, order = "pruningwise") + .C("node_depth_edgelength", as.integer(n), as.integer(n), + as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]), + as.integer(N), as.double(phy$edge.length), double(n + m), + DUP = FALSE, PACKAGE = "ape")[[7]] +} + +node.height <- function(phy) +{ + n <- length(phy$tip.label) + m <- phy$Nnode + N <- dim(phy$edge)[1] + phy <- reorder(phy, order = "pruningwise") + + e1 <- phy$edge[, 1] + e2 <- phy$edge[, 2] + + yy <- numeric(n + m) + TIPS <- e2[e2 <= n] + yy[TIPS] <- 1:n + + .C("node_height", as.integer(n), as.integer(m), + as.integer(e1), as.integer(e2), as.integer(N), + as.double(yy), DUP = FALSE, PACKAGE = "ape")[[6]] +} + +node.height.clado <- function(phy) +{ + n <- length(phy$tip.label) + m <- phy$Nnode + N <- dim(phy$edge)[1] + phy <- reorder(phy, order = "pruningwise") + + e1 <- phy$edge[, 1] + e2 <- phy$edge[, 2] + + yy <- numeric(n + m) + TIPS <- e2[e2 <= n] + yy[TIPS] <- 1:n + + .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), DUP = FALSE, + PACKAGE = "ape")[[7]] +} + plot.multiPhylo <- function(x, layout = 1, ...) { if (layout > 1)