plotQualityProfile {dada2} | R Documentation

## 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"))

[Package dada2 version 1.20.0 Index]