R/scales.R

In gjuggler/ape: Analyses of Phylogenetics and Evolution

## scales.R (2009-12-16)

##   Add a Scale Bar or Axis to a Phylogeny Plot

## add.scale.bar: add a scale bar to a phylogeny plot
## axisPhylo: add a scale axis on the side of a phylogeny plot

## Copyright 2002-2009 Emmanuel Paradis

## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.

add.scale.bar <- function(x, y, length = NULL, ask = FALSE, ...)
{
    lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
    direc <- lastPP$direction
    if (is.null(length)) {
        nb.digit <-
          if (direc %in% c("rightwards", "leftwards")) diff(range(lastPP$xx))
          else diff(range(lastPP$yy))
        nb.digit <- ceiling(log10(nb.digit)) - 2
        length <- eval(parse(text = paste("1e", nb.digit, sep = "")))
    }

    if (ask) {
        cat("\nClick where you want to draw the bar\n")
        x <- unlist(locator(1))
        y <- x[2]
        x <- x[1]
    } else if (missing(x) || missing(y)) {
        if (lastPP$type %in% c("phylogram", "cladogram")) {
            switch(direc,
                   "rightwards" = {
                       x <- 0
                       y <- 1
                   },
                   "leftwards" = {
                       x <- max(lastPP$xx)
                       y <- 1
                   },
                   "upwards" = {
                       x <- max(lastPP$xx)
                       y <- 0
                   },
                   "downwards" = {
                       x <- 1
                       y <- max(lastPP$yy)
                   })
        } else {
            direc <- "rightwards" # just to be sure for below
            x <- lastPP$x.lim[1]
            y <- lastPP$y.lim[1]
        }
    }

    switch(direc,
           "rightwards" = {
               segments(x, y, x + length, y)
               text(x + length * 1.1, y, as.character(length), adj = c(0, 0.5), ...)
           },
           "leftwards" = {
               segments(x - length, y, x, y)
               text(x - length * 1.1, y, as.character(length), adj = c(1, 0.5), ...)
           },
           "upwards" = {
               segments(x, y, x, y + length)
               text(x, y + length * 1.1, as.character(length), adj = c(0, 0.5), srt = 90, ...)
           },
           "downwards" = {
               segments(x, y - length, x, y)
               text(x, y - length * 1.1, as.character(length), adj = c(0, 0.5), srt = 270, ...)
           })
}

axisPhylo <- function(side = 1, ...)
{
    lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
    if (lastPP$type %in% c("phylogram", "cladogram")) {
        if (lastPP$direction %in% c("rightwards", "leftwards")) {
            x <- pretty(lastPP$xx)
            if (lastPP$direction == "rightwards") maxi <- max(lastPP$xx)
            else {
                maxi <- min(lastPP$xx)
                x <- -x
            }
        } else {
            x <- pretty(lastPP$yy)
            if (lastPP$direction == "upwards") maxi <- max(lastPP$yy)
            else {
                maxi <- min(lastPP$yy)
                x <- -x
            }
        }
    }
    axis(side = side, at = c(maxi - x), labels = abs(x), ...)
}