phylosim (version 3.0.2)

plot.ToleranceSubstitution: Create a bubble plot of the substitution process

Description

Create a bubble plot of the substitution process.

Bubble plots visualize the characteristics of the substitution process. The area of the circles is proportional to the rates/probabilities. The plot is not produced if the rate matrix or the equlibrium distribution has undefined elements.

Usage

# S3 method for ToleranceSubstitution
plot(x, scale=1, ...)

Arguments

x

An object inheriting from ToleranceSubstitution.

scale

A scale factor affecting the area of the circles.

...

Not used.

Value

The process object (invisible).

See Also

For more information see ToleranceSubstitution.

Examples

# NOT RUN {
	plot(BinarySubst(rate.list=list("0->1"=1,"1->0"=1.5)))
	plot(JC69())
	# get smaller circles
	plot(JC69(),scale=0.5)
	plot(F84(base.freqs=c(3/6,1/6,1/6,1/6)))
	plot(WAG())
 
# }