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\name{matchDistribution}
\alias{matchDistribution}
\alias{matchDistribution,Axt-method}
\title{
Plot the distribution of matched alignments.
}
\description{
Given a \code{Axt} alignment, plot a heatmap showing the percentage of
each matched alignments.
}
\usage{
matchDistribution(x, size=10000, title=NULL)
}
\arguments{
\item{x}{
\code{Axt} object.
}
\item{size}{
\code{integer}(1): the number of alignments to use. By default, it is 10000.
}
\item{title}{
\code{character}(1): the customised title for the plot.
}
}
\details{
By default, if there are more than 10,000 alignments,
10,000 alignments will be sampled and calculated for the distribution
for speed purposes.
Only the four bases (A, C, G, T), gap (-) and any (N) are displayed.
Other ambiguous bases are not considered.
}
\value{
A ggplot2 object will be returned.
}
\author{
Ge Tan
}
\examples{
axtFile <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
axt <- readAxt(axtFile)
matchDistribution(axt)
}
|
