plotComplexity {dada2} | R Documentation

## Plot sequence complexity profile of a fastq file.

### Description

This function plots a histogram of the distribution of sequence complexities in the form of effective numbers of kmers as determined by `seqComplexity`. By default, kmers of size 2 are used, in which case a perfectly random sequences will approach an effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size).

### Usage

    plotComplexity(
      fl,
      kmerSize = 2,
      window = NULL,
      by = 5,
      n = 1e+05,
      bins = 100,
      aggregate = FALSE,
      ...
    )

### Arguments

`fl` | (Required). `character`. File path(s) to fastq or fastq.gz file(s).
`kmerSize` | (Optional). Default 2. The size of the kmers (or "oligonucleotides" or "words") to use.
`window` | (Optional). Default NULL. The width in nucleotides of the moving window. If NULL the whole sequence is used.
`by` | (Optional). Default 5. The step size in nucleotides between each moving window tested.
`n` | (Optional). Default 100,000. The number of records to sample from the fastq file.
`bins` | (Optional). Default 100. The number of bins to use for the histogram.
`aggregate` | (Optional). Default FALSE. If TRUE, compute an aggregate quality profile for all fastq files provided.
`...` | (Optional). Arguments passed on to `geom_histogram`.

### Value

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

### See Also

`seqComplexity` `oligonucleotideFrequency`

### Examples

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

[Package dada2 version 1.20.0 Index]