\name{plot.deepSNV}
\alias{plot.deepSNV}
\title{Scatter plot of relative nucleotide frequencies.}
\usage{\method{plot}{deepSNV}(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, ...)}
\description{Scatter plot of relative nucleotide frequencies.}
\details{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 \eqn{- \log}{-log} of the p-value.}
\value{NULL}
\author{gemoritz}
\arguments{\item{x}{A deep SNV object.}
\item{sig.level}{By default, p-values below sig.level are drawn as filled circles.}
\item{col}{Color of the nucleotides.}
\item{col.null}{Color of insignificant nucleotides.}
\item{cex.min}{The minimal size of the points.}
\item{xlab}{The x-axis label.}
\item{ylab}{The y-axis label.}
\item{pch}{The plotting symbol. Default = 16 (filled circle)}
\item{...}{Additional arguments passed to plot.}
}
\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))}