plot.db: Plot a dualbrothers object

In vnminin/rbrothers: rbrothers: multiple change-point recombination detection

Description

This function creates two plots from a DualBrothers object. The first plots the posterior probability of each tree as a function of base pair position. The second plots the posterior probability of a break point as a function of base pair position.

Usage

## S3 method for class 'db'
plot(x,makepic="FALSE",ext="png",seetrees="FALSE",numplot=4,

                  type="unrooted",linewidth=1,colors=NULL,threshold=0,...)

Arguments

x	a DualBrothers object
makepic	a string, either "FALSE" or "TRUE", if "TRUE" the two plots are outputted into a .png file in the current working directory
ext	a string, either "png" or "pdf", when makepic is TRUE determines what type of file to produce
seetrees	a string, either "FALSE" or "TRUE", if "TRUE" the second plot show the trees instead of the posterior probability of a breakpoint
numplot	an integer, determines the number of trees to display in the second plot (only used if seestrees is "TRUE")
type	a string specifying the type of phylogeny to be drawn; it must be one of "phylogram", "cladogram", "fan", "unrooted", "radial" or any unambiguous abbreviation of these (only used if seestrees is "TRUE")
linewidth	a number, determines the thickness of the lines on the posterior probability plot
colors	a vector of color names to determine the palette for plotting
threshold	posterior probability threshold, a number between 0 and 1, only those trees that attained a posterior probability greater than the number provided will be plotted
...	optional arguments

Value

Two posterior probability plots

vnminin/rbrothers documentation built on May 3, 2019, 6:38 p.m.