Learn R Programming

R453Plus1Toolbox (version 1.22.0)

nucleotideCharts: Nucleotide Charts

Description

This function plots the relative frequency of the four bases for each position in the sequences.

Usage

nucleotideCharts(object, range=0.95, linetypes=c(A="l", C="l", G="l", T="l", N="l"), linecols=c(A="black", C="red", G="blue", T="green", N="grey70"), xlab="Position", ylab="Frequency", ...)

Arguments

object
An object of class DNAStringSet, ShortRead or SFFContainer.
range
An integer vector of length one or two. If length one only bases up to the percent quantile of read lengths defined by the given value are shown. A vector of length two gives the start and end base between which the nucleotide frequencies are plotted.
linetypes
The line types used for the four nucleotids + N, see (see ‘par’)
linecols
The colors in which the four nucleotids + N should be plotted.
xlab
The X axis label.
ylab
The Y axis label.
...
Arguments to be passed to methods, such as graphical parameters (see ‘par’).