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

Description Usage Arguments Value Author(s) See Also Examples

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

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## 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

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	# 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")
 


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