plotBases-methods {qrqc} | R Documentation |
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.
plotBases(obj, type="freq", bases=NULL, legend=TRUE)
obj |
an S4 object of class that inherits from
|
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 |
legend |
a logical value indicating whether to include a legend on the top right. |
Vince Buffalo <vsbuffalo@ucdavis.edu>
## 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)