tax_datatable: Make a datatable with the taxonomy of a 'phyloseq-class'...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Make a datatable with the taxonomy of a phyloseq-class object

Description

An interactive table for phyloseq taxonomy.

Usage

tax_datatable(
  physeq,
  abundance = TRUE,
  taxonomic_level = NULL,
  modality = NULL,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
abundance	(default: TRUE) Does the number of sequences is print
taxonomic_level	(default: NULL) a vector of selected taxonomic level using their column numbers (e.g. taxonomic_level = 1:7)
modality	(default: NULL) A sample modality to split OTU abundancy by level of the modality
...	Other argument for the datatable function

Value

A datatable

Author(s)

Adrien Taudière

Examples

data("GlobalPatterns", package = "phyloseq")
if (requireNamespace("DT")) {
  tax_datatable(subset_taxa(
    GlobalPatterns,
    rowSums(GlobalPatterns@otu_table) > 10000
  ))

  # Using modality
  tax_datatable(GlobalPatterns,
    modality = GlobalPatterns@sam_data$SampleType
  )
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.