barplot.bam: Draw/calculate a barplot showing the length distribution of...

In mw55309/viRome_legacy: Analysis and visualisation of short-read sequencing data from virus-infection studies

Description

This function counts the occurrence of reads of a given size range mapping to the positive and negative strands of a reference sequence.

Generally, users of viRome may be interested in how many 21-22bp (viRNA) and 24-29bp (piRNA) reads align to the reference genome, on both the positive and negative strand.

Usage

barplot.bam(vdf = NULL, minlen = 1, maxlen = 37, poscol="red", negcol="green", main = "Sequence length distribution", xlab = "Map length", ylab = "Count", legend = c("+ve strand", "-ve strand"),
legendx = NULL, legendy = NULL, plot=TRUE, down=FALSE, sym.axes=TRUE,  ...)

Arguments

vdf	A data.frame as produced by read.bam and clip.bam
minlen	The minimum length of aligned read to consider
maxlen	The maximum length of aligned read to consider
poscol	The colour of the "positive" bars. Defaults to "red"
negcol	The colour of the "negative" bars. Defaults to "green"
main	Title for the plot
xlab	Labels for the x-axis
ylab	Labels for the y-axis
legend	Vector of text for the positive and negative strand in the legend
legendx	The x location for the legend
legendy	The y location for the legend
plot	Whether or not to draw a plot. Set this to "FALSE" to suppress plotting.
down	Whether or not the plot for the negative strand should be plotted downwards. Defaults to FALSE.
sym.axes	If down is TRUE, this determines whether the x-axis is symmetrical around zero. Defaults to TRUE
...	Further parameters to pass to the barplot function

Details

A barplot is plotted, and the summarised data returned as a data.frame. Set plot=FALSE to suppress plotting.

Value

A barplot is plotted, and the data returned as a data.frame

lgth	The length of the aligned read
pos	Count of alignments on the positive strand
neg	Count of alignments on the negative strand

Author(s)

Mick Watson

See Also

read.bam, clip.bam

Examples

 ## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
 ## Not run: bam <- read.bam(bamfile=infile, chr="SINV", start=1, end=11703, removeN=TRUE)
 ## Not run: bamc <- clip.bam(bam)

 ## Not run: bi <- barplot.bam(vdf=bamc, minlen=1, maxlen=37)
 ## Not run: bi

 ## Not run: bp <- barplot.bam(bamc)
 ## Not run: bp <- barplot.bam(bamc, down=TRUE)


 ## Not run: bp <- barplot.bam(bamc, space=c(0,0))
 ## Not run: bp <- barplot.bam(bamc, down=TRUE, space=c(0,0))


 ## Not run: bp <- barplot.bam(bamc, down=TRUE, space=c(0,0), minlen=17, maxlen=36, legendx=17)

mw55309/viRome_legacy documentation built on Dec. 21, 2021, 11:05 p.m.