plotCNEDistribution: Plot sequential CNE number against CNE genomic location

In ge11232002/CNEr: CNE Detection and Visualization

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

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))

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.