plotAmpliconCoverage: Creates a plot visualizing the number of reads per amplicon

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

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)

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.