plotVariationFrequency {R453Plus1Toolbox} | R Documentation

## 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)

### Author(s)

Hans-Ulrich Klein

### Examples

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

[Package R453Plus1Toolbox version 1.40.0 Index]