plotParametersAtSites.Sequence: Plot the value of a site-process specifc paramter for a...

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object. The type of the paramter must be numeric. The Process object must be attached to all positions specified in the index vector.

Usage

## S3 method for class 'Sequence'
plotParametersAtSites(this, process, id, index, ...)

Arguments

this	A Sequence object.
process	A Process object.
id	The identifier of the site-process specific parameter.
index	An integer vector specifying a set of positions. It is set to 1:seq$length if omitted.
...	Not used.

Value

Invisible TRUE or FALSE.

Author(s)

Botond Sipos, Gregory Jordan

See Also

Site Process Sequence

Examples

	# create a nucleotide sequence with a process attached
	p<-JC69()
	s<-NucleotideSequence(string="ATGGCCA",processes=list(list(p)))
	# plot rate multipliers in range 1:4
	plotParametersAtSites(s,p,"rate.multiplier",1:4)
	# plot rate multiplier for the full sequence
	plotParametersAtSites(s,p,"rate.multiplier")
 

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