stat_coverage {ggbio} | R Documentation

## Calculate coverage

### Description

Calculate coverage.

### Usage

    # for GRanges
    ## S4 method for signature 'GRanges'
    stat_coverage(data, ..., xlim, xlab, ylab, main,
                  facets = NULL, geom = NULL)
    # for GRangesList
    ## S4 method for signature 'GRangesList'
    stat_coverage(data, ..., xlim, xlab, ylab, main,
                  facets = NULL, geom = NULL)

    # for Bamfile
    ## S4 method for signature 'BamFile'
    stat_coverage(data, ..., maxBinSize = 2^14,
                   xlim, which, xlab, ylab,
                   main, facets = NULL, geom = NULL,
                   method = c("estimate", "raw"),
                   space.skip = 0.1, coord = c("linear", "genome"))

### Arguments

`data` | A `GRanges` or `data.frame` object.
`...` | Extra parameters such as aes() passed to `geom_rect`, `geom_alignment`, or `geom_segment`.
`xlim` | Limits for x.
`xlab` | Label for x
`ylab` | Label for y
`main` | Title for plot.
`facets` | Faceting formula to use.
`geom` | The geometric object to use display the data.
`maxBinSize` | maxBinSize.
`method` | 'estimate' for parsing estimated coverage(fast), 'raw' is slow and parse the accurate coverage.
`which` | `GRanges` which defines region to subset the results.
`space.skip` | used for coordinate genome, skip between chromosomes.
`coord` | coordinate system.

### Value

A 'Layer'.

### Author(s)

Tengfei Yin

### Examples

    library(ggbio)
    ## ======================================================================
    ##  simmulated GRanges
    ## ======================================================================
    set.seed(1)
    N <- 1000
    library(GenomicRanges)

    gr <- GRanges(seqnames =
                  sample(c("chr1", "chr2", "chr3"),
                         size = N, replace = TRUE),
                  IRanges(
                          start = sample(1:300, size = N, replace = TRUE),
                          width = sample(70:75, size = N,replace = TRUE)),
                  strand = sample(c("+", "-", "*"), size = N,
                    replace = TRUE),
                  value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
                  sample = sample(c("Normal", "Tumor"),
                    size = N, replace = TRUE),
                  pair = sample(letters, size = N,
                    replace = TRUE))

    ggplot(gr) + stat_coverage()
    ggplot() + stat_coverage(gr)

    ggplot(gr) + stat_coverage(geom = "point")
    ggplot(gr) + stat_coverage(geom = "area")
    ggplot(gr) + stat_coverage(aes(y = ..coverage..), geom = "bar")

    ggplot(gr) + stat_coverage(aes(y = ..coverage..)) + geom_point()

    ## for bam file
    ## TBD

[Package ggbio version 1.42.0 Index]