plotCNEDistribution {CNEr} | R Documentation

## 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))

[Package CNEr version 1.20.0 Index]