R453Plus1Toolbox (version 1.22.0)

plotVariationFrequency: Create an AVA style variation frequency plot

Description

This method creates a plot similar to the variation frequency plot in Roche's GS Amplicon Variant Analyzer. The plot shows the reference sequence along the x-axis and indicates variants as bars at the appropriate positions. The height of the bars corresponds to the percentage of reads carrying the variant. A second y-axis indicates the absolute number of reads covering the variant.

Usage

plotVariationFrequency(object, plotRange, ...)

Arguments

object

A character pointing to an Amplicon Variant Analyser Global Alignmnet export file.

plotRange

A two dimensional numeric vector giving the start and end base of the reference sequence that should be plotted.

...

Arguments passed to other plotting methods. Especially, argument col: Optional character vector of length 7 specifying the bars' colors indicating different base substitutions or deletions. See details. And argument sequenceCex: Optional numeric value specifying the size of the reference sequence's bases.

Details

The text file used as imput must have the format generated by the AVA export function. Such a file can be generated using the export button in the Global Alignment view of the AVA software. The col argument specifies the colours used for different bases and deletions. The following listing gives the meaning of the i-th position of the col vector (default values in braces):

1. A (green)
2. C (blue)
3. G (black)
4. T (red)
5. N (purple)
6. deletion (gray)

Examples

## Not run: 
# file = system.file("extdata", "AVAVarFreqExport", "AVAVarFreqExport.xls", package="R453Plus1Toolbox")
# plotVariationFrequency(file, plotRange=c(50, 150))## End(Not run)