size.strand.bias.plot: Plot counts of read lengths on + and - strands

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

Description

This simple function takes the output of barplot.bam and plots counts of read length on the + and - strand against one another. It can be used to visually inspect the data to see if there is a strand bias for particular read lengths

Usage

size.strand.bias.plot(bp = NULL, minlen = 1, maxlen = 37, line.col = "red", sym.axes = TRUE, title = "Strand bias plot", xlab = "+ strand counts", ylab = "- strand counts", lty = 1, lwd = 2, cextxt = 1, mar = c(5, 4, 4, 1), tpos = 1, ...)

Arguments

bp	The output from barplot.bam
minlen	The minimum length of aligned read to consider
maxlen	The maximum length of aligned read to consider
line.col	The colour of the y=x line to plot (default: "red")
sym.axes	Whether or not the X- and Y- axes should be symmetrical
title	A title for the plot
xlab	A label for the x-axis
ylab	A label for the y-axis.
lty	The line type. Line types can either be specified as an integer (0=blank, 1=solid (default), 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "blank", "solid", "dashed", "dotted", "dotdash", "longdash", or "twodash", where "blank" uses ‘invisible lines’ (i.e., does not draw them).
lwd	The line width, a positive number, defaulting to 1. The interpretation is device-specific, and some devices do not implement line widths less than one.
cextxt	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. Use this to adjust the size of the labels in the plot
mar	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.
tpos	Control the position of the text label relative to the point. Values of 1, 2, 3 and 4, respectively indicate positions below, to the left of, above and to the right of the specified coordinates.
...	Further graphical paramters to be passed to the plot() function

Value

A plot is created on the current device.

Author(s)

Mick Watson <[e-mail]>

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: bp <- barplot.bam(bamc)
 ## Not run: size.strand.bias.plot(bp)

 ## Not run: size.strand.bias.plot(bp, mar=c(4,4,3,1), pch=".", tpos=3, cextxt=0.8)

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