chrom.barplot: Reads per chromosome barplot

Description

Barplot of numbers (or fractions) of reads (and targets) falling on each chromosome

Usage

chrom.barplot(reads, targets, plotchroms, col = c("darkgreen", "orange"), ylab, legendpos = "topright", ...)

Arguments

reads

RangedData table containing read positions, i.e. output from get.reads. To ensure a useful ordering of the bars, the chromosome information ('spaces' of reads) should be given as "chr" plus a number/letter [plus further specification], e.g. "chr1", "chrX", "chr17_ctg5_hap1", "chrUn_gl000211".

targets

Optional RangedData table containing positions of target regions, i.e. output from get.targets. The chromosome information should match the one of reads. If targets is missing, only numbers of reads will be displayed.

plotchroms

character vector specifying the chromosomes that shall be included in the plot (and their desired order)

col

color(s) of the bars

ylab

y-axis label

legendpos

Position of the legend. String from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Ignored if targets is missing.

...

graphical parameters passed to barplot

Value

Details

If targets is not specified, absolute read counts per chromosome are shown in the barplot. If targets is provided, fractions of reads and targets are shown. For reads, this is the fraction within the total number of reads (since reads are expected to have all the same length). In contrast, for the targets, the fraction of targeted bases on each chromosome is calculated. Since targets might vary in length it is reasonable to account for the actual target sizes instead of considering merely numbers of targets per chromosome.

Examples

Run this code

## 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)

chrom.barplot(reads, targets)