plot_seq_len_hist

This function takes a tibble produced by `fasta_reader()` or `fastq_reader()`
and plots the distribution of sequence lengths.

A series of R functions that come in handy while working with metabarcoding data.
The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way.
In a way it is all about putting together the grammar of the 'tidyverse' from Wickham et al.(2019) <doi:10.21105/joss.01686>
with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x>
and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>.
The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'),
to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package
works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.

Ramón Gallego Simón

eDNAfuns

Working with Metabarcoding Data in a Tidy Format

plot_seq_len_hist function

<dl><dt>Hash_tibble</dt>
<dd>A tibble containing a numeric column with sequence lengths.</dd>
<dt>length_col</dt>
<dd>The column of `Hash_tibble` containing sequence lengths (unquoted).</dd>
<dt>binwidth</dt>
<dd>Width of histogram bins. Default = 1.</dd>
<dt>label_interval</dt>
<dd>Interval for x-axis labels. Default = 5.</dd></dl>

Arguments

Plot sequence length distribution — plot_seq_len_hist

<dl>

<dt>Hash_tibble</dt>
<dd>A tibble containing a numeric column with sequence lengths.</dd>


<dt>length_col</dt>
<dd>The column of `Hash_tibble` containing sequence lengths (unquoted).</dd>


<dt>binwidth</dt>
<dd>Width of histogram bins. Default = 1.</dd>


<dt>label_interval</dt>
<dd>Interval for x-axis labels. Default = 5.</dd>

</dl>

plot_seq_len_hist: Plot sequence length distribution

Description

Usage

Value

Arguments

Examples