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\name{plotCNEDistribution}
\alias{plotCNEDistribution}
\title{
Plot sequential CNE number against CNE genomic location
}
\description{
Plot the CNE genomic location distribution.
It gives an overview of the tendency of CNEs to form clusters.
}
\usage{
plotCNEDistribution(x, chrs = NULL, chrScale = c("Mb", "Kb"))
}
\arguments{
\item{x}{
\code{GRanges} object: the CNE locations.
}
\item{chrs}{
\code{character}(n): the chromosomes to show. By default,
the largest 6 chromosomes/scaffolds are selected.
}
\item{chrScale}{
\code{character}(1): the chromosome/scaffold scale of \sQuote{Mb}
or \sQuote{Kb} in the plot.
}
}
\details{
In the plot, x axis is the genomic location along each chromosome/scaffold.
The y axis is the sequential CNE number.
A typical CNE cluster can be spotted by the dramatic increase in y axis and
small increase in x axis.
}
\value{
A \code{ggplot} object.
}
\author{
Ge Tan
}
\seealso{
\code{\link{plotCNEWidth}}
}
\examples{
dbName <- file.path(system.file("extdata", package="CNEr"),
"danRer10CNE.sqlite")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
cneGRangePairs <- readCNERangesFromSQLite(dbName=dbName,
tableName="danRer10_hg38_45_50",
tAssemblyFn=tAssemblyFn,
qAssemblyFn=qAssemblyFn)
plotCNEDistribution(first(cneGRangePairs))
}
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