QA-utils: Plotting functions for quality objects
In jotsetung/SeqUtils: Utility functions for high throughput sequencing

Description Usage Arguments Methods and Functions Author(s) See Also Examples

These functions allow to plot or retrieve summary statistics for quality assessment objects generated by the qa2 function of the ShortRead package.

## S4 method for signature 'QA'
overview(x, ...)

## S4 method for signature 'QAReadQuality'
plot(x, y, subset=NULL, ...)

## S4 method for signature 'QANucleotideByCycle'
plot(x, y, dnaCol=c("#1F78B4",
"#33A02C", "#B2DF8A", "#A6CEE3", "#E31A1C"), subset=NULL, ...)

## S4 method for signature 'QAQualityByCycle'
plot(x, y, type="levelplot", subset=NULL, ...)

## S4 method for signature 'QANucleotideUse'
plot(x, y, dnaCol=c("#1F78B4", "#33A02C",
"#B2DF8A", "#A6CEE3", "#E31A1C"), subset=NULL, ...)

## S4 method for signature 'QAQualityUse'
plot(x, y, subset=NULL, ...)

## S4 method for signature 'QASequenceUse'
plot(x, y, ...)

## S4 method for signature 'QAQualityUse'
plotDensity(x, xlab="Used base-call quality",
ylab="density", col, pal=brewer.pal(8, "Set1"), lty=1, subset=NULL, ...)

## S4 method for signature 'QANucleotideUse'
table(x, ...)

## S4 method for signature 'QAFrequentSequence'
table(x, ...)

## S4 method for signature 'QAAdapterContamination'
table(x, ...)

(in alphabetic order)

`...`	Additional arguments.
`col`	Allows to specify the colors for the individual sequencing runs manually.
`dnaCol`	The colors that for the individual nucleotides (A, C, G, T and N).
`lty`	For `plotDensity`: the line type.
`pal`	Vector of colors that can be used to define the colors for the individual sequencing runs. Colors might be recycled.
`subset`	Generate the plot for a subset of data. Argument `subset` has to be a numeric vector with the indices of the files for which the plot should be generated. The default will generate the plot for all files.
`type`	For `QAQualityByCycle`: allowed values: `"levelplot"` and `"boxplot"`. If the base call quality information per cycle should be visualized as a levelplot or boxplot.
`x`	The QA object (see function `qa2` in the `ShortRead` package).
`xlab`	For `plotDensity`: the x-axis label.
`y`	Not used by any of the functions.
`ylab`	For `plotDensity`: the y-axis label.

overview: Returns a data.frame with some information about the analyzed fastq files.
plot: Creates a plot summarizing the quality information from the corresponding QA object (see qa2 for a full list of QA objects).

plotDensity Draws a density plot representing the signal distribution.

table

returns summary statistics for the corresponding QA object:

For QAFrequentSequence: A data.frame with columns Id, Records, Seq_count and Sequence for the sample ID, the number of records (reads) for that sample, the number of occurences of the sequence and the sequence.
For QANucleotideUse: A data.frame with the total count of nucleotides as well as the percentage of nucleotide use in all sequences of the sample.

Johannes Rainer

qa2

#############
## Examples:
##
## Perform a quality assessment on a fastq file:
dirpath <- system.file(package="SeqUtils", "extdata")
fastqs <- dir(dirpath, "example.fastq.gz", full=TRUE)

## collating the quality controls:
coll <- QACollate(
    QAFastqSource(con=fastqs, n=10e+06),
    QAReadQuality(),
    QAAdapterContamination(),
    QANucleotideUse(),
    QAQualityUse(),
    QASequenceUse(),
    QAFrequentSequence(n=10),
    QANucleotideByCycle(),
    QAQualityByCycle()
   )
## perform the quality control
qualy <- qa2(coll, verbose = TRUE)


############
## overview
overview(qualy)

############
## distribution of average base call quality per read
plot(qualy$QAReadQuality)


############
## nucleotide quality by cycle:
plot(qualy$QANucleotideByCycle)


###########
## base call quality by cycle
plot(qualy$QAQualityByCycle)
plot(qualy$QAQualityByCycle, type="boxplot")


###########
## nucleotide use
plot(qualy$QANucleotideUse)

## in addition return the table with the actual values (and percentages)
table(qualy$QANucleotideUse)


##########
## base call quality use
plot(qualy$QAQualityUse)

## plot the base call quality as density distributions
plotDensity(qualy$QAQualityUse)


##########
## sequence use
plot(qualy$QASequenceUse)


#########
## frequent sequence
table(qualy$QAFrequentSequence)


#########
## adapter contamination
table(qualy$QAAdapterContamination)