MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

reorder_taxa_pq

R Documentation

Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object

Description

Note that the taxa order in a physeq object with a tree is locked by the order of leaf in the phylogenetic tree.

Usage

reorder_taxa_pq(physeq, names_ordered, remove_phy_tree = FALSE)

Arguments

`physeq`	(required): a `phyloseq-class` object obtained using the `phyloseq` package.
`names_ordered`	(required): Names of the taxa (must be the same as taxa in `taxa_names(physeq)`) in a given order
`remove_phy_tree`	(logical, default FALSE) If TRUE, the phylogenetic tree is removed. It is

Value

A phyloseq object

Author(s)

Adrien Taudière

Examples


data_fungi_ordered_by_genus <- reorder_taxa_pq(
  data_fungi,
  taxa_names(data_fungi)[order(as.vector(data_fungi@tax_table[, "Genus"]))]
)

data_fungi_mini_asc_ordered_by_abundance <- reorder_taxa_pq(
  data_fungi_mini,
  taxa_names(data_fungi_mini)[order(taxa_sums(data_fungi_mini))]
)

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