skylineplot: Drawing Skyline Plot Graphs

Description

These functions provide various ways to draw skyline plot graphs on the current graphical device. Note that skylineplot(z, ...) is simply a shortcut for plot(skyline(z, ...)). The skyline plot itself is an estimate of effective population size through time, and is computed using the function skyline.

Usage

## S3 method for class 'skyline':
plot(x, show.years=FALSE, subst.rate, present.year, \dots)
## S3 method for class 'skyline':
lines(x, show.years=FALSE, subst.rate, present.year, \dots)
skylineplot(z, ...)
skylineplot.deluxe(tree, ...)

Arguments

skyline plot data (i.e. an object of class "skyline").

Either an ultrametric tree (i.e. an object of class "phylo"), or coalescent intervals (i.e. an object of class "coalescentIntervals"), or collapsed coalescent intervals (i.e. an object of class "collapsedInt

tree

ultrametric tree (i.e. an object of class "phylo").

show.years

option that determines whether the time is plotted in units of of substitutions (default) or in years (requires specification of substution rate and year of present).

subst.rate

substitution rate (see option show.years).

present.year

present year (see option show.years).

...

further arguments to be passed on to skyline() and plot().

Details

See skyline for more details (incl. references) about the skyline plot method.

Examples

Run this code

library(ape)

# get tree
data("hivtree.newick") # example tree in NH format
tree.hiv <- read.tree(text = hivtree.newick) # load tree


#### classic skyline plot
skylineplot(tree.hiv) # shortcut


#### plot classic and generalized skyline plots and estimate epsilon
sk.opt <- skylineplot.deluxe(tree.hiv) 
sk.opt$epsilon


#### classic and generalized skyline plot ####
sk1 <- skyline(tree.hiv)   
sk2 <- skyline(tree.hiv, 0.0119) 

# use years rather than substitutions as unit for the time axis
plot(sk1, show.years=TRUE, subst.rate=0.0023, present.year = 1997, col=c(grey(.8),1))
lines(sk2,  show.years=TRUE, subst.rate=0.0023, present.year = 1997)
legend(.15,500, c("classic", "generalized"), col=c(grey(.8),1),lty=1)


#### various skyline plots for different epsilons
layout(mat= matrix(1:6,2,3,byrow=TRUE))
ci <- coalescent.intervals(tree.hiv)
plot(skyline(ci, 0.0));title(main="0.0")
plot(skyline(ci, 0.007));title(main="0.007")
plot(skyline(ci, 0.0119),col=4);title(main="0.0119")
plot(skyline(ci, 0.02));title(main="0.02")
plot(skyline(ci, 0.05));title(main="0.05")
plot(skyline(ci, 0.1));title(main="0.1")
layout(mat= matrix(1:1,1,1,byrow=TRUE))

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