plotCoverage {RIPSeeker} | R Documentation

## Plot read coverage for a GRanges object

### Description

An internal function used by `plotStrandedCoverage` to plot read counts within each fixed bin across the entire chromosome.

### Usage

    plotCoverage(x, plotLegend = FALSE, legend.cex = 1, ...)

### Arguments

`x` | GRanges object with values slot saved for read counts within the corresponding ranges.
`plotLegend` | Binary indcator. If TRUE, legend will be plotted on the top left the plot. Legend is expected to be the chromsome name and length, which must be available in the GRange object argument.
`legend.cex` | Font size of the legend.
`...` | Extra arguments passed to either the `plot` or the `legend`.

### Details

The read counts is plotted in blue bars as positive integer across the x-axis as the sorted positions across the chromosome. The plot can be used to examine the overall alignment properties for each chromosome.

### Note

Users are not recommanded run this function directly but rather via a much more user friendly function `plotStrandedCoverage`.

### Author(s)

Yue Li

### References

P. Aboyoun, H. Pages and M. Lawrence (). GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

### See Also

`plotStrandedCoverage, plot, legend`

### Examples

    # Retrieve system files
    extdata.dir <- system.file("extdata", package="RIPSeeker")

    bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

    bamFiles <- grep("PRC2", bamFiles, value=TRUE)

    alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

    alignGR <- as(alignGal, "GRanges")

    alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

    binSize <- 1000

    binGR <- binCount(alignGRList$chrX, binSize)

    plotCoverage(binGR, plotLegend=TRUE)

[Package RIPSeeker version 1.20.0 Index]