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Last data update: 2014.03.03

R: Coverage versus base position plot

coverage.plot

R Documentation

Coverage versus base position plot

Description

Line plot of per-base coverages along a genomic region. Position of target regions can be shown.

Usage

coverage.plot(coverageAll, targets, chr, Start, End, Offset = 0, add = FALSE, col.line = 1, col.target = "orange", col.offset = "yellow", xlab, ylab, ylim, ...)

Arguments

`coverageAll`	`RleList` containing `Rle` vectors of per-base coverages for each chromosome, i.e. `coverageAll` output from `coverage.target`
`targets`	optional; `RangedData` table containing positions of target regions, i.e. output from `get.targets`; if missing no genomic regions are highlighted
`chr`	on which chromosome the region to plot is located (string, e.g. "chr1")
`Start`	genomic position where to start the plot
`End`	genomic position where to end the plot
`Offset`	integer; highlight `Offset` bases on both sides of each targeted region; defaults to 0
`add`	if `TRUE`, the coverage line of a new sample is added to an already existing plot
`col.line`	color of the coverage line
`col.target`	color of the bar indicating target regions
`col.offset`	color for highlighting `Offset` on the sides of target regions
`xlab, ylab`	x- and y-axis labels
`ylim`	y-axis coordinate ranges
`...`	further graphical parameters, passed to `plot`

Details

If coverage of a new sample is added to an existing plot with add = TRUE, parameters chr, Start, End still have to be specified and should be the same as in the previous call in order to make sense. Parameters targets and Offset can but do not have to be given again. They can also differ from the previous ones, if for the additional sample a different target was captured.

Value

Line plot showing per-base read coverages for a specified genomic region. When positions of target regions are provided, a bar on the bottom indicates their location such that coverage can be related to the captured targets.

Author(s)

Manuela Hummel m.hummel@dkfz.de

Examples

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## coverage plot
coverage.plot(Coverage$coverageAll, targets, Offset=100, chr="chr1", Start=11157524, End=11158764)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(TEQC)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: hwriter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TEQC/coverage.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverage.plot
> ### Title: Coverage versus base position plot
> ### Aliases: coverage.plot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## get reads and targets
> exptPath <- system.file("extdata", package="TEQC")
> readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
> reads <- get.reads(readsfile, idcol=4, skip=0)
[1] "read 19546 sequenced reads"
> targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
> targets <- get.targets(targetsfile, skip=0)
[1] "read 50 (non-overlapping) target regions"
Warning message:
the "reduce" method for RangedData object is deprecated 
> 
> ## calculate per-base coverages
> Coverage <- coverage.target(reads, targets, perBase=TRUE)
> 
> ## coverage plot
> coverage.plot(Coverage$coverageAll, targets, Offset=100, chr="chr1", Start=11157524, End=11158764)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>