ggbio (version 1.20.1)

stat_coverage: Calculate coverage

Description

Calculate coverage.

Usage

# for GRanges
## S3 method for class 'GRanges':
stat_coverage(data, ..., xlim, xlab, ylab, main,
              facets = NULL, geom = NULL)
# for GRangesList
## S3 method for class 'GRangesList':
stat_coverage(data, ..., xlim, xlab, ylab, main,
              facets = NULL, geom = NULL)
# for Bamfile
## S3 method for class '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'.

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