plotBases: Plot Bases by Position

Description Usage Arguments Author(s) See Also Examples

Description

plotBases plots the frequency or proportion of bases by position in the read.

plotBases uses the Sanger base color scheme: blue is Cytosine, green is Adenine, black is Guanine, red is Thymine, and purple in N (any base). Other IUPAC nucleotides are colored using RColorBrewer.

Usage

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  plotBases(obj, type="freq", bases=NULL, legend=TRUE)

Arguments

obj

an S4 object of class that inherits from SequenceSummary (either FASTASummary or FASTQSummary) from readSeqFile.

type

a character string that is either "freq" or "prop" indicating whether to plot frequencies or proportions on the y-axis.

bases

a vector of characters indicating which bases to include. The default value NULL indicates to plot _all_ bases.

legend

a logical value indicating whether to include a legend on the top right.

Author(s)

Vince Buffalo <[email protected]>

See Also

basePlot

Examples

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## Not run: 
  ## Load a FASTQ file, with sequence hashing.
  s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))

  ## Plot base frequencies
  plotBases(s.fastq, type="freq")

  ## Plot base proportions
  plotBases(s.fastq, type="prop")

## End(Not run)

qrqc documentation built on Nov. 17, 2017, 9:55 a.m.