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Clean Taxonomy Table in Phyloseq Object

Source: R/tax_clean.R
tax_clean.Rd

This function cleans and filters the taxonomy table within a phyloseq object. It removes unclassified or ambiguous names, and replaces these and missing taxon names at genus level with placeholders derived from higher taxonomic ranks. Optionally this function filters specific taxa (e.g., Eukaryota, chloroplasts, mitochondria, and ASVs unclassified at Kingdom and Phylum levels). The cleaned taxonomy enables taxonomic agglomeration (tax_glom form the package phyloseq) to genus level without merging unclassified taxa from diverse ancestry.

Usage

tax_clean(physeq = physeq, tax_filter = TRUE)

Arguments

physeq

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

tax_filter

Iindicating whether to apply additional filtering to remove unwanted taxa (e.g., chloroplasts, mitochondria).

  • TRUE: Apply filtering to remove taxa such as Eukaryota, chloroplasts, mitochondria, and unclassified taxa.

  • FALSE: Skip filtering; the taxonomy table will only be cleaned but no taxa will be removed.

Value

A cleaned phyloseq object with ambiguous and unwanted taxa removed or replaced. The cleaned phyloseq object is saved as an RDS file named <project_name>_phyloseq_cleaned.rds in the output_data/rds_files/Before_cleaning_rds_files directory.

Details

The function performs the following steps:

  • Cleans the taxonomy table:

    • Replaces ambiguous or placeholder taxa names (e.g., "uncultured organism") with NA.

    • Assigns missing taxon names based on their higher-level ranks (e.g., "Phylum of Kingdom").

    • Cleans the taxonomic ranks to remove overly nested placeholders.

    • Ensures consistent naming for Kingdom (e.g., replacing "d__Bacteria" with "Bacteria").

  • If tax_filter = TRUE, filters out unwanted taxa such as:

    • Chloroplasts (at Class or Order level).

    • Mitochondria (at Family level).

    • Unassigned taxa or taxa classified as Eukaryota.

  • Saves the cleaned phyloseq object as an RDS file.

  • Logs the number of ASVs (amplicon sequence variants) removed during cleaning.

The cleaned phyloseq object is returned for further analysis.

Examples

if (FALSE) { # \dontrun{
# Clean taxonomy table and apply filtering
physeq_cleaned <- tax_clean(physeq = physeq, tax_filter = TRUE)

# Clean taxonomy table without filtering
physeq_cleaned_no_filter <- tax_clean(physeq = physeq, tax_filter = FALSE)
} # }