phylosim (version 3.0.5)

plotParametersAtSites.Sequence: Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object

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 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.

See Also

Site Process Sequence

Examples

# NOT RUN {
	# 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")
 
# }