plot_refseq_pq: Plot the nucleotide proportion of references sequences

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot the nucleotide proportion of references sequences

Description

It is a wrapper of the function plot_refseq_extremity_pq(). See ?plot_refseq_extremity_pq for more examples.

If hill_scale is not null, Hill diversity number are used to represent the distribution of the diversity (equitability) along the sequences.

Usage

plot_refseq_pq(
  physeq,
  q = NULL,
  first_n = min(Biostrings::width(physeq@refseq)),
  last_n = NULL,
  min_width = first_n
)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
q	(vector) A vector defining the Hill number wanted. Set to NULL if you don't want to plot Hill diversity metrics. Hill numbers are more appropriate in DNA metabarcoding studies when q > 0 (Alberdi & Gilbert, 2019; Calderón-Sanou et al., 2019).
first_n	(int, default 10) The number of nucleotides to plot the 5' extremity.
last_n	(int, default 10) The number of nucleotides to plot the 3' extremity.
min_width	(int, default 0) Select only the sequences from physeq@refseq with using a minimum length threshold. If first_n is superior to the minimum length of the references sequences, you must use min_width to filter out the narrower sequences

Value

A ggplot2 object

Author(s)

Adrien Taudière

Examples

plot_refseq_pq(data_fungi_mini)
## Not run: 
plot_refseq_pq(data_fungi_mini, q = c(2), first_n = 300)

## End(Not run)

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.