## scales.R (2008-02-08)

##   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 2002-2008 Emmanuel Paradis

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

add.scale.bar <- function(x = 0, y = 1, length = NULL, ...)
{
    if (is.null(length)) {
        nb.digit <- ceiling(log10(mean(get("last_plot.phylo$xx",
                                           envir = .PlotPhyloEnv)))) - 2
        length <- eval(parse(text = paste("1e", nb.digit, sep = "")))
    }
    segments(x, y, x + length, y)
    text(x + length * 1.1, y, as.character(length), adj = c(0, 0.5), ...)
}

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