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Last data update: 2014.03.03

R: Plot distribution of errors by read position.

ReadPosErrorPlot

R Documentation

Plot distribution of errors by read position.

Description

Plots the number of sequencing errors by read position.

Usage

ReadPosErrorPlot(ReadPosErrors, startpos = 1, error_col = "blue", thresh = 1.5, 
   thresh_col = "cyan", xlabel = "Read Position", ylabel = "# Errors", 
   main_title = "Distribution of Errors by Read Position")

Arguments

`ReadPosErrors`	vector of sequencing error counts by read position.
`startpos`	Starting read position, typically 0 or 1. Default = 1.
`error_col`	color of line plotting the errors counts. Default = "blue".
`thresh`	Threshold for identifying read positions with large numbers of errors, plotted as a horizontal dashed line. Threshold is set as “thresh * (average number of errors per read position)”. Default = 1.5.
`thresh_col`	color of threshold line. Default = "cyan".
`xlabel`	x-axis label. Default = "Read Position".
`ylabel`	y-axis label. Default = "# Errors".
`main_title`	title. Default = "Distribution of Errors by Read Position".

Details

ReadPosErrorPlot plots the distribution of sequencing errors by read position. If the input vector is $ReadPosErrors from ReQON output, this function will create the top left 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 error counts 
x <- c( 1:30 )
err <- x^2 + ( 30 - x )^1.6 + rnorm(30, 0, 100)

## plot errors by read position
ReadPosErrorPlot( err )

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/ReadPosErrorPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ReadPosErrorPlot
> ### Title: Plot distribution of errors by read position.
> ### Aliases: ReadPosErrorPlot
> 
> ### ** Examples
> 
> ## Create data of error counts 
> x <- c( 1:30 )
> err <- x^2 + ( 30 - x )^1.6 + rnorm(30, 0, 100)
> 
> ## plot errors by read position
> ReadPosErrorPlot( err )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>