R/skylineplot.R

In ape: Analyses of Phylogenetics and Evolution

## skylineplot.R (2004-07-4)

##   Various methods to plot skyline objects (= skyline plots)

## Copyright 2002-2004 Korbinian Strimmer

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

# plot skyline
plot.skyline <- function(x, show.years=FALSE, subst.rate, present.year, ...)
{
  if (!inherits(x, "skyline"))
    stop("object \"x\" is not of class \"skyline\"")
  t <- x$time
  m <- x$population.size
  lm <- length(m)

  if (show.years)
  {
    plot((-c(0,t))/subst.rate+present.year,c(m,m[lm]),type="s",
     xlab="time (years)",ylab="effective population size",log="y", ...)

  }
  else
  {
    plot(c(0,t),c(m,m[lm]),type="s", xlim=c(t[lm],0),
     xlab="time (past to present in units of substitutions)",ylab="effective population size",log="y", ...)
  }

}

# plot another skyline plot on top
lines.skyline <- function(x, show.years=FALSE, subst.rate, present.year, ...)
{
  if (!inherits(x, "skyline"))
    stop("object \"x\" is not of class \"skyline\"")
  t <- x$time
  m <- x$population.size
  lm <- length(m)


  if (show.years)
  {
    lines((-c(0,t))/subst.rate+present.year,c(m,m[lm]),type="s", ...)
  }
  else
  {
    lines(c(0,t),c(m,m[lm]),type="s", ...)
  }
}


# convenience short cut (almost compatible with APE 0.1)
skylineplot <- function(z, ...) plot(skyline(z, ...))


#input: phylogenetic tree
skylineplot.deluxe <- function(tree, ...)
{
  if (!inherits(tree, "phylo"))
    stop("object \"tree\" is not of class \"phylo\"")

  ci <- coalescent.intervals(tree)
  classic <- skyline(ci)
  generalized <- skyline(ci, -1)
  plot(classic,col=grey(.8), ...)
  lines(generalized, ...)
  return(generalized)
}