tbl_sum_taxtable: Summarize a tax_table (taxonomic slot of phyloseq object)...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Summarize a tax_table (taxonomic slot of phyloseq object) using gtsummary

Description

Mainly a wrapper for the gtsummary::tbl_summary() function in the case of physeq object.

Usage

tbl_sum_taxtable(physeq, taxonomic_ranks = NULL, ...)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
taxonomic_ranks	A list of taxonomic ranks we want to summarized.
...	Other arguments passed on to gtsummary::tbl_summary()

Value

A table of class c('tbl_summary', 'gtsummary')

Author(s)

Adrien Taudière

Examples

tbl_sum_taxtable(data_fungi_mini)
data_fungi_mini |>
  filt_taxa_pq(min_occurence = 2) |>
  tbl_sum_taxtable(taxonomic_rank = c("Species", "Genus"))

adrientaudiere/MiscMetabar documentation built on Feb. 7, 2025, 5:47 p.m.