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

Source: R/table_functions.R
tax_datatable.Rd

lifecycle-maturing

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

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
  )
}
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’