FWSEplot {ReQON} | R Documentation

## Plot reported vs. empirical quality.

### Description

Plots reported vs. empirical quality scores. Also calculates and outputs Frequency-Weighted Squared Error (FWSE) and reports FWSE on the plot. The points are shaded according to the relative frequency of bases assigned that quality score.

### Usage

    FWSEplot(ErrRates, QualFreq, FWSE_out = TRUE, col = "blue", max_freq = 0.25,
       lim = c(0, length(QualFreq) - 1), collegend = TRUE, xlabel = "Reported Quality",
       ylabel = "Empirical Quality", main_title = "Reported vs. Empirical Quality")

### Arguments

`ErrRates` | vector of empirical error rates on the Phred scale.
`QualFreq` | vector of relative frequencies of quality scores.
`FWSE_out` | option to output FWSE and report FWSE on the plot. Default = TRUE.
`col` | color of plotted points. Currently allows for only "blue" and "red". Default = "blue".
`max_freq` | Maximum value for color scale, where all quality scores with relative frequency greater than this value are shaded the darkest color. Because the colors are evenly distributed between 0 and max_freq, changing this maximum value may change the color of many points. Default = 0.25.
`lim` | common axis limits for both the x-axis and y-axis. Default = c(0, length(QualFreq) - 1).
`collegend` | include color legend. Default = TRUE.
`xlabel` | x-axis label. Default = "Reported Quality".
`ylabel` | y-axis label. Default = "Empirical Quality".
`main_title` | title. Default = "Reported vs. Empirical Quality".

### Details

FWSEplot plots the reported quality score against the empirical quality score and reports FWSE. If the quality scores accurately reflect the probability of a sequencing error, then the points should fall close to the 45-degree line and FWSE should be close to zero. If the input vectors are $ErrRatesBefore and $QualFreqBefore from the ReQON output, this function will create the bottom left diagnostic plot that is output from ReQON. Similarly, if the input vectors are $ErrRatesAfter and $QualFreqAfter from ReQON output, then the bottom right diagnostic plot is created.

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

### Value

In addition to the plot, FWSEplot calculates and outputs Frequency-Weighted Squared Error (FWSE), a measure of how close the points lie to the 45-degree line.

### Author(s)

Christopher Cabanski ccabansk@genome.wustl.edu

### Examples

    ## Create relative frequency example data
    require( stats )
    after <- dnorm( c( 0:40 ), mean = 30, sd = 8 )
      after <- after / sum( after )
    err_rate <- c( 0:40 ) + rnorm( 41, mean = 0, sd = 5)
      err_rate[ which( err_rate < 0 ) ] <- (-1) * err_rate[ which( err_rate < 0 ) ]
      ## to guarantee that all values are positive

    ## plot and calculate FWSE
    FWSEplot( err_rate, after, col = "red" )

[Package ReQON version 1.28.0 Index]