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

In phylosim: Flexible Simulations of Biological Sequence Evolution

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 class 'GeneralSubstitution'
plot(x, scale=1, ...)

Arguments

x	An object inheriting from GeneralSubstitution.
scale	A scale factor affecting the area of the circles.
...	Not used.

Value

The process object (invisible).

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see GeneralSubstitution.

Examples

	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())
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.