coverage.plot: Coverage versus base position plot

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/coverage.plot.R

Description

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

Usage

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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

See Also

coverage.target, make.wigfiles, covered.k, coverage.hist, coverage.uniformity, coverage.targetlength.plot

Examples

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## 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)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

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

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

Attaching package:S4VectorsThe following object is masked frompackage:base:

    expand.grid

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package:BiostringsThe following object is masked frompackage:base:

    strsplit

Loading required package: hwriter
[1] "read 19546 sequenced reads"
[1] "read 50 (non-overlapping) target regions"

TEQC documentation built on Nov. 8, 2020, 8:07 p.m.