Plot frequency distributions of quality scores.

Description

Plots the relative frequency distribution of quality scores before and after recalibration.

Usage

QualFreqPlot(QualFreqBefore, QualFreqAfter, before_col = "blue", 
   after_col = "red", inc_legend = TRUE, xlabel = "Quality Score", 
   ylabel = "Relative Frequency", 
   main_title = "Frequency Distributions of Quality Scores")

Arguments

Details

QualFreqPlot plots the relative frequency distribution of quality scores before and after recalibration. If the input vectors are $QualFreqBefore and $QualFreqAfter from ReQON output, this function will create the top right diagnostic plot that is output from ReQON.

For more details and interpretation, see the vignette by: browseVignettes("ReQON").

Author(s)

Christopher Cabanski ccabansk@genome.wustl.edu

Examples

## Create data of frequencies
require( stats )
before <- dpois( c( 0:40 ), 40 )
  before <- before / sum( before )
after <- dnorm( c( 0:40 ), mean = 30, sd = 8 )
  after <- after / sum( after )

## plot
QualFreqPlot( before, after )

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(ReQON)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: seqbias
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ReQON/QualFreqPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: QualFreqPlot
> ### Title: Plot frequency distributions of quality scores.
> ### Aliases: QualFreqPlot
> 
> ### ** Examples
> 
> ## Create data of frequencies
> require( stats )
> before <- dpois( c( 0:40 ), 40 )
>   before <- before / sum( before )
> after <- dnorm( c( 0:40 ), mean = 30, sd = 8 )
>   after <- after / sum( after )
> 
> ## plot
> QualFreqPlot( before, after )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>