enrichmentPlot {Repitools} | R Documentation

## Plot the distribution of sequencing enrichment.

### Description

Function to generate a plot of the distribution of sequencing reads enrichments.

### Usage

      ## S4 method for signature 'GRangesList'
    enrichmentPlot(x, seq.len, cols = rainbow(length(x)),
          xlim = c(0, 20), main = "Enrichment Plot", total.lib.size = TRUE, verbose = TRUE, ...)

### Arguments

`x` | A `GRangesList` object of reads to plot enrichment of. The chromosome lengths must be stored in the `Seqinfo` of this object.
`seq.len` | The fragment size to be used for extending the sequencing reads.
`cols` | The line colour for each element of `x`
`xlim` | `xlim` parameter passed to `plot`, the default is appropriate for `"linear"` `cpgDensityCalc` weighting.
`main` | `main` parameter passed to `plot`
`total.lib.size` | Whether to normalise enrichment values to the total number of reads per lane.
`verbose` | Print details of processing.
`...` | Additional graphical parameters to pass to `plot`.

### Details

See `enrichmentCalc` for details of how the results are determined.

### Value

A plot is created. The data processed by `enrichmentCalc` is invisibly returned.

### Author(s)

Aaron Statham

### Examples

      data(samplesList)  # GRangesList of reads 'samples.list.subset'
      enrichmentPlot(samples.list.subset, seq.len = 300, total.lib.size = FALSE)

[Package Repitools version 1.30.0 Index]