plotData: Plot an Rprimer object

In sofpn/rprimer: Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Plot an Rprimer object

Description

plotData visualizes objects from all different Rprimer classes.

Usage

plotData(x, ...)

## S4 method for signature 'RprimerProfile'
plotData(x, type = "overview", highlight = NULL, rc = FALSE)

## S4 method for signature 'RprimerOligo'
plotData(x)

## S4 method for signature 'RprimerAssay'
plotData(x)

## S4 method for signature 'RprimerMatchOligo'
plotData(x)

## S4 method for signature 'RprimerMatchAssay'
plotData(x)

Arguments

x	An RprimerProfile, RprimerOligo RprimerAssay, rprimerMatchOligo or RprimerMatchAssay object.
...	Optional arguments for RprimerProfile objects.
type	For Rprimeroligo objects: Type of plot: "overview", or "nucleotide", defaults to "overview".
highlight	For Rprimeroligo objects: If a specific region within an overview plot should be highlighted. A numeric vector indicating the start and end position, e.g. c(100, 1000), defaults to NULL (i.e., no highlight).
rc	For Rprimeroligo objects, and type = "nucleotide": If the plotted sequence should be displayed as reverse complement or not. TRUE or FALSE, defaults to FALSE. See examples below.

Value

A plot.

Methods (by class)

• plotData(RprimerProfile):

• plotData(RprimerOligo):

• plotData(RprimerAssay):

• plotData(RprimerMatchOligo):

• plotData(RprimerMatchAssay):

Examples

#### Plot an RprimerProfile object

data("exampleRprimerProfile")
prof <- exampleRprimerProfile

## Plot an overview
plotData(prof, highlight = c(500, 1000))

## Select a region of interest
roi <- prof[prof$position >= 500 & prof$position <= 550, ]

## Plot an overview of the roi
plotData(roi)

## Plot the nucleotide distribution of the roi
plotData(roi, type = "nucleotide")

#### Plot an RprimerOligo object

data("exampleRprimerOligo")
plotData(exampleRprimerOligo)

#### Plot an RprimerAssay object

data("exampleRprimerAssay")
plotData(exampleRprimerAssay)

#### Plot an RprimerMatchOligo object

data("exampleRprimerMatchOligo")
plotData(exampleRprimerMatchOligo)

#### Plot an RprimerMatchAssay object

data("exampleRprimerMatchAssay")
plotData(exampleRprimerMatchAssay)

sofpn/rprimer documentation built on July 2, 2023, 7:15 a.m.