plot.job {BayesPeak} | R Documentation

## Plot the called peaks in a job.

### Description

Plot the distribution of reads in a .bed file, with BayesPeak's calls highlighted.

### Usage

    plot.job(x, raw.out, job, strand = "+", threshold = 0.5,
    	xlim = c(0,1), highlight = TRUE, col.un = "grey",
    	col.enr = "blue", bin = 100L, ...)

### Arguments

`x` | RangedData (from the IRanges package) with a value column entitled `"strand"`. The .bed file to plot. This could have been read in with `read.bed`, or alternatively by the `import` function in the rtracklayer library.
`raw.out` | Raw output from the `bayespeak` function.
`job` | Integer. The number of the job to plot.
`strand` | Character. Strand to plot - usually either "+" or "-". If the `bed` argument uses a different convention in its strand column, this can be used instead.
`threshold` | Numeric. Bins with a PP higher than this value will be classed as enriched.
`xlim` | Numeric vector. This controls which part of the job is plotted. For example, `c(0.5,1)` would plot the last half of the job, whereas `c(0.25,0.75)` would plot the central half.
`highlight` | Logical. FIXME
`col.un` | The colour used to plot counts in unenriched bins.
`col.enr` | The colour used to plot counts in enriched bins.
`bin` | What sized bin should be used? Currently, this value should be the same as the value used in `bayespeak`. The function will behave strangely if this parameter is altered, particularly to pathological values.
`...` | Additional arguments to be passed through to `hist`.

### Details

Similar to `plot.bed`, `plot.job` takes the reads in a bed file, and plots a histogram of their locations - i.e. plots the bin counts. It then goes on to highlight the histogram bins that have been made in the raw.output from `bayespeak`.

It is worth bearing in mind that BayesPeak takes the information on both strands into account when calling peaks, and therefore judgements based on a one-stranded view of the data should be treated with caution. For a better picture of what is going on, both strands should be viewed simultaneously, as is done in the examples below.

### Value

Plots a histogram on the active graphical device.

### Author(s)

Jonathan Cairns

### References

Spyrou C, Stark R, Lynch AG, Tavare S BayesPeak: Bayesian analysis of ChIP-seq data, BMC Bioinformatics 2009, 10:299 doi:10.1186/1471-2105-10-299

### See Also

`bayespeak`, `read.bed`, `plot.bed`.

### Examples

    ##get the ChIP .bed file
    dir <- system.file("extdata", package="BayesPeak")
    treatment <- file.path(dir, "H3K4me3reduced.bed")
    bed <- read.bed(treatment)

    ##get the corresponding raw.output object
    data(raw.output.H3K4me3)

    ##plot job 1, + and - strand
    par(mfrow = c(2,1))
    plot.job(bed, raw.output.H3K4me3, 1)
    plot.job(bed, raw.output.H3K4me3, 1, "-")

    ##zoom in for a closer look...
    plot.job(bed, raw.output.H3K4me3, 1, xlim = c(0.58,0.6))
    plot.job(bed, raw.output.H3K4me3, 1, "-", xlim = c(0.58,0.6))

[Package BayesPeak version 1.38.0 Index]