R453Plus1Toolbox (version 1.22.0)

plotAmpliconCoverage: 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

"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.

See Also

AVASet

Examples

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