tree_glom: Agglomerate taxa at a given phylogenetic resolution.

In mikemc/speedyseq: Faster implementations of phyloseq functions

Agglomerate taxa at a given phylogenetic resolution.

Description

This function merges taxa that are sufficiently closely related in the tree in phy_tree(physeq). It is similar to tip_glom(), except that it uses the tree directly, rather than as the basis for hierarchical clustering.

Usage

tree_glom(physeq, resolution, criterion = "max_tip_depth", tax_adjust = 1L)

Arguments

physeq	phyloseq-class() or ape::phylo().
resolution	Phylogenetic resolution at which to merge taxa.
criterion	Criterion for determining whether to collapse taxa. See castor::collapse_tree_at_resolution() for details.
tax_adjust	0: no adjustment; 1: phyloseq-compatible adjustment; 2: conservative adjustment (see merge_taxa_vec() for details)

Details

This function uses castor::collapse_tree_at_resolution() from the castor package to determine the groups of taxa to be collapsed; see this function for details about the resolution and criterion parameters.

New taxa are named according to the most abundant taxon of each group. The tree, reference sequences, and (by default) the taxonomy table reflect these "archetype" taxa.

Value

A physeq object with new taxa reflecting the phylogenetically merged groups.

See Also

castor::collapse_tree_at_resolution() for more information about the resolution and criterion parameters.

merge_taxa_vec() for more about tax_adjust and general merging behavior

tip_glom() for indirect phylogenetic merging

tax_glom() for merging using taxonomy

Examples

data(GlobalPatterns)
ps1 <- subset_taxa(GlobalPatterns, Phylum == "Chlamydiae")
ntaxa(ps1)
ps2 <- tree_glom(ps1, 0.05)
ntaxa(ps2)

suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(ggtree))
suppressPackageStartupMessages(library(cowplot))

plot1 <- phy_tree(ps1) %>%
  ggtree +
  geom_tiplab() +
  geom_label(aes(x = branch, label = round(branch.length, 4)))
plot2 <- phy_tree(ps2) %>%
  ggtree +
  geom_tiplab() +
  geom_label(aes(x = branch, label = round(branch.length, 4)))
plot_grid(plot1, plot2)

mikemc/speedyseq documentation built on April 22, 2024, 6:40 p.m.