rotl wrapper for phyloseq data — rotl

Make a taxonomic tree using the ASV names of a physeq object and the Open Tree of Life tree.

Usage

rotl_pq(
  physeq,
  taxonomic_rank = c("Genus", "Species"),
  context_name = "All life",
  discard_genus_alone = TRUE,
  pattern_to_remove_tip = c("ott\\d+|_ott\\d+"),
  pattern_to_remove_node = c("_ott.*|mrca*")
)

Arguments

physeq: (required) a phyloseq-class object obtained using the phyloseq package.
taxonomic_rank: (Character) The column(s) present in the @tax_table slot of the phyloseq object. Can be a vector of two columns (e.g. the default c("Genus", "Species")). If only one column is set it need to be format in this way ("Genus species" for ex. "Quercus robur") with a space.
context_name: : can bue used to select only a part of the Open Tree of Life. See ?rotl::tnrs_contexts() for available values
discard_genus_alone: (logical) If TRUE (default), genus without information at the species level are discarded.
pattern_to_remove_tip: (character regex string) A regex to remove unwanted part of tip names. If set to null, tip names are left intact.
pattern_to_remove_node: (character regex string) A regex to remove unwanted part of node names. If set to null, node names are left intact.

Value

A plot

Details

This function is mainly a wrapper of the work of others. Please make a reference to rotl package if you use this function.

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
if (requireNamespace("rotl")) {
  tr <- rotl_pq(data_fungi_mini, pattern_to_remove_tip = NULL)
  plot(tr)

  tr_Asco <- rotl_pq(data_fungi,
    taxonomic_rank = c("Genus", "Species"),
    context_name = "Ascomycetes"
  )
  plot(tr_Asco)
}
} # }