Summarize a phyloseq-class object using a plot. — summary_plot

Graphical representation of a phyloseq object.

Usage

summary_plot_pq(
  physeq,
  add_info = TRUE,
  min_seq_samples = 500,
  clean_pq = TRUE,
  text_size = 1,
  text_size_info = 1
)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
add_info: Does the bottom down corner contain extra informations?
min_seq_samples: (int): Used only when add_info is set to true to print the number of samples with less sequences than this number.
clean_pq: (logical): Does the phyloseq object is cleaned using the clean_pq() function?
text_size: (Num, default 1) A size factor to expand or minimize text size.
text_size_info: (Num, default 1) A size factor to expand or minimize text size for extra informations.

Value

A ggplot2 object

Examples


summary_plot_pq(data_fungi)

summary_plot_pq(data_fungi, add_info = FALSE) + scale_fill_viridis_d()
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.

if (requireNamespace("patchwork")) {
  (summary_plot_pq(data_fungi, text_size = 0.5, text_size_info = 0.6) +
    summary_plot_pq(data_fungi_mini, text_size = 0.5, text_size_info = 0.6)) /
    (summary_plot_pq(data_fungi_sp_known, text_size = 0.5, text_size_info = 0.6) +
      summary_plot_pq(subset_taxa(data_fungi_sp_known, Phylum == "Ascomycota"),
        text_size = 0.5, text_size_info = 0.6
      ))
}
#> Cleaning suppress 0 taxa and 1 samples.
#> Cleaning suppress 0 taxa and 2 samples.