plot.deepSNV: Scatter plot of relative nucleotide frequencies.
In mg14/deepSNV-old: Detection of subclonal SNVs in deep sequencing data.

Description Usage Arguments Author(s) Examples

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.

## 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, ...)

`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.
`xlab`	The x-axis label.
`ylab`	The y-axis label.
`pch`	The plotting symbol. Default = 16 (filled circle)
`...`	Additional arguments passed to plot.

Moritz Gerstung

## 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))