stat_coverage-method: Calculate coverage

In lawremi/ggbio: Visualization tools for genomic data

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

lawremi/ggbio documentation built on Nov. 1, 2023, 2:40 p.m.