plotAmpliconCoverage {R453Plus1Toolbox} | R Documentation

## Creates a plot visualizing the number of reads per amplicon

### Description

A function for visualizing the number of reads per amplicon or per MID / pico titer plate.

### Usage

    ## S4 method for signature 'AVASet,character,logical'
    plotAmpliconCoverage(avaSet, type="amplicon", bothDirections=TRUE, cex.names=0.8, cex.axis=0.8, las=3, col=c(rgb(217/255, 214/255, 209/255), rgb(173/255, 38/255, 36/255)), ...)

### Arguments

`avaSet` | An instance of AVASet.
`type` | A character vector specifying the type of plot.
`bothDirections` | A logical value determining whether the plot sums forward and reverse reads or shows them separately.
`cex.names` | Font size of the amplicon name labels.
`cex.axis` | Font size of axes' labels.
`las` | Orientation of amplicon name labels.
`col` | Colors used in the plot.
`...` | Arguments to be passed to methods, such as graphical parameters (see ‘par’).

### Details

If the argumnet type is “amplicon”, the number of reads for each amplicon are visualized. In case of a AVASet with one sample, a barplot with one bar for each amplicon is created. In case of more than one sample, a boxplot with one box for each amplicon is plotted. If type is “mid”, a boxplot with one box for each MID is created. If type is “ptp”, a boxplot with one box for each pico titer plate is created.

### Author(s)

Hans-Ulrich Klein

### See Also

`AVASet`

### Examples

    ## Not run: data(avaSetExample)
    plotAmpliconCoverage(avaSetExample)
    plotAmpliconCoverage(avaSetExample[,1])
    ## End(Not run)

[Package R453Plus1Toolbox version 1.40.0 Index]