plotCNEDistribution: Plot sequential CNE number against CNE genomic location

In CNEr: CNE Detection and Visualization

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

x	GRanges object: the CNE locations.
chrs	character(n): the chromosomes to show. By default, the largest 6 chromosomes/scaffolds are selected.
chrScale	character(1): the chromosome/scaffold scale of ‘Mb’ or ‘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 ggplot object.

Author(s)

Ge Tan

See Also

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))

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.