Plot GC Content by Position

Description

gcPlot plots the GC content by position in the read.

Usage

  gcPlot(x, color="red")

Arguments

Methods

signature(x = "FASTQSummary")

gcPlot will plot the GC content for a single object that inherits from SequenceSummary.

signature(x = "list")

gcPlot will plot the GC content for each of the SequenceSummary items in the list and display them in a series of panels.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

getBase, getBaseProp

Examples

  ## Load a FASTQ file, with sequence hashing.
  s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))

  ## Plot GC content
  gcPlot(s.fastq)

  ## Plot multiple GC content plots
  s.trimmed.fastq <- readSeqFile(system.file('extdata',
    'test-trimmed.fastq', package='qrqc'))
  gcPlot(list("not trimmed"=s.fastq, "trimmed"=s.trimmed.fastq))

  ## Graphical features can be added
  gcPlot(s.trimmed.fastq) + geom_hline(yintercept=0.5, color="purple")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(qrqc)
Loading required package: reshape
Loading required package: ggplot2
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:reshape':

    expand, rename

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: biovizBase
Loading required package: brew
Loading required package: xtable
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: testthat

Attaching package: 'testthat'

The following object is masked from 'package:S4Vectors':

    compare

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/qrqc/gcPlot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: gcPlot-methods
> ### Title: Plot GC Content by Position
> ### Aliases: gcPlot gcPlot-methods gcPlot,list-method
> ###   gcPlot,SequenceSummary-method
> ### Keywords: methods graphics
> 
> ### ** Examples
> 
>   ## Load a FASTQ file, with sequence hashing.
>   s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))
> 
>   ## Plot GC content
>   gcPlot(s.fastq)
> 
>   ## Plot multiple GC content plots
>   s.trimmed.fastq <- readSeqFile(system.file('extdata',
+     'test-trimmed.fastq', package='qrqc'))
>   gcPlot(list("not trimmed"=s.fastq, "trimmed"=s.trimmed.fastq))
> 
>   ## Graphical features can be added
>   gcPlot(s.trimmed.fastq) + geom_hline(yintercept=0.5, color="purple")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>