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Resolve Multichotomies in Phyloseq Object's Tree

Source: R/resolve_tree.R
resolve_tree.Rd

This function processes the phylogenetic tree within a phyloseq object by resolving polytomous branching in the QIIME2 FastTree2 phylogeny, converting it into a fully bifurcated (binary) tree using the ape package for phylogenetic analysis. This step is essential for accurate evolutionary analysis, and the updated phyloseq object is saved as an RDS file.

Usage

resolve_tree(physeq = cleaned_physeq)

Arguments

physeq

A phyloseq object containing the microbiome data. This is the input object that the function processes.

Value

A phyloseq object with a binary phylogenetic tree. The phyloseq with a binary phylogenetic tree is saved as an RDS file named <project_name>_phyloseq_resolved_tree.rds in the output_data/rds_files/Before_cleaning_rds_files directory.

Details

This function performs the following steps:

  • Checks if the phyloseq object contains a binary phylogenetic tree.

  • Resolves polychotomous nodes (if present) using ape::multi2di().

  • Ensures that the tree is binary after resolution; raises an error if unresolved.

  • Merges the resolved tree back with the otu_table, sample_data, and tax_table in the phyloseq object.

  • Saves the updated phyloseq object with the resolved tree as an RDS file.

Examples

if (FALSE) { # \dontrun{
# Resolve tree and save the updated phyloseq object
resolved_physeq <- resolve_tree(physeq = cleaned_physeq)
} # }