Plot the nucleotide proportion of references sequences

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,
  hill_scales = 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.

hill_scales

(vector) A vector defining the Hill number wanted. Set to NULL if you don't want to plot Hill diversity metrics.

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

Adrien Taudière

Examples

plot_refseq_pq(data_fungi)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 1
#> Number of kept ASV 1419
#> Number of kept samples 185
#> Cleaning suppress 0 taxa and 0 samples.
#> Warning: Removed 688 rows containing missing values or values outside the scale range
#> (`geom_point()`).

plot_refseq_pq(data_fungi, hill_scales = c(2), first_n = 300)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 483
#> Number of kept ASV 937
#> Number of kept samples 185
#> Cleaning suppress 0 taxa and 0 samples.
#> Warning: Removed 492 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 123 rows containing missing values or values outside the scale range
#> (`geom_line()`).