plot.deepSNV {deepSNV} | R Documentation

## Scatter plot of relative nucleotide frequencies.

### Description

This function plots the relative nucleotide frequencies of the test against the control experiment on a logarithmit scale. The color of the symbols denotes the nucleotide, and the area of the circle is proportional to the -log of the p-value.

### Usage

    ## S3 method for class 'deepSNV'
    plot(
      x,
      sig.level = NULL,
      col = NULL,
      col.null = "grey",
      cex.min = 0.2,
      ylab = "Relative Frequency in Test",
      xlab = "Relative Frequency in Control",
      pch = 16,
      ...
    )

### Arguments

`x` | A deep SNV object.
`sig.level` | By default, p-values below sig.level are drawn as filled circles.
`col` | Color of the nucleotides.
`col.null` | Color of insignificant nucleotides.
`cex.min` | The minimal size of the points.
`ylab` | The y-axis label.
`xlab` | The x-axis label.
`pch` | The plotting symbol. Default = 16 (filled circle)
`...` | Additional arguments passed to plot.

### Author(s)

Moritz Gerstung

### Examples

    ## Short example with 2 SNVs at frequency ~10%
    regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140)
    ex <- deepSNV(test = system.file("extdata", "test.bam", package="deepSNV"), control = system.file("extdata", "control.bam", package="deepSNV"), regions=regions, q=10)
    show(ex)   # show method
    plot(ex)   # scatter plot
    summary(ex)   # summary with significant SNVs
    ex[1:3,]   # subsetting the first three genomic positions
    tail(test(ex, total=TRUE))   # retrieve the test counts on both strands
    tail(control(ex, total=TRUE))

    ## Not run: Full example with ~ 100 SNVs. Requires an internet connection, but try yourself.
    # regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585)
    # HIVmix <- deepSNV(test = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", control = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", regions=regions, q=10)
    data(HIVmix) # attach data instead..
    show(HIVmix)
    plot(HIVmix)
    head(summary(HIVmix))

[Package deepSNV version 1.40.0 Index]