dada2: plotQualityProfile – R documentation

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plotQualityProfile

Plot quality profile of a fastq file.

Description

This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq file(s).

Usage

plotQualityProfile(fl, n = 5e+05, aggregate = FALSE)

Arguments

`fl`	(Required). `character`. File path(s) to fastq or fastq.gz file(s).
`n`	(Optional). Default 500,000. The number of records to sample from the fastq file.
`aggregate`	(Optional). Default FALSE. If TRUE, compute an aggregate quality profile for all fastq files provided.

Details

The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles.

If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend to at least that position.

Value

A ggplot2 object. Will be rendered to default device if printed, or can be stored and further modified. See ggsave for additional options.

Examples

plotQualityProfile(system.file("extdata", "sam1F.fastq.gz", package="dada2"))

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

v1.18.0

LGPL-3

Authors

Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes

Initial release

2020-08-07