Compare and Analyse Multiple phyloseq Objects • comparpq

comparpq is an extension to the {MiscMetabar} and {phyloseq} packages that provides tools for comparing phyloseq objects. The package focuses on taxonomic comparison, accuracy metrics computation, and interactive visualizations for microbiome data analysis.

Installation

You can install the released version of comparpq from CRAN with:

install.packages("comparpq")

You can install the development version of comparpq from GitHub with:

# install.packages("devtools")
devtools::install_github("adrientaudiere/comparpq")

Main Features

Taxonomic Comparison and Accuracy Metrics

tc_metrics_mock(): Compute accuracy metrics comparing taxonomic assignations against mock communities
tc_metrics_mock_vec(): Vectorized version for efficient metric computation
tc_points_matrix(): Create matrices for taxonomic comparison visualization

Visualization Tools

bubbles_pq(): Interactive bubble plots using Observable HQ for phyloseq objects
tc_bar() & tc_circle(): Bar charts and circular plots for taxonomic comparisons
rainplot_taxo_na(): Rain plots for visualizing NA patterns in taxonomic data

Data Manipulation

Fake taxa creation: add_external_seq_pq(), add_shuffle_seq_pq() for mock community preparation
Taxonomic table utilities: rename_ranks_pq(), select_ranks_pq(), resolve_taxo_conflict()
Pattern replacement: taxtab_replace_pattern_by_NA() for data cleaning

Quick Start

library(comparpq)

# Load example data
data("Glom_otu")

# Create an interactive bubble plot
bubbles_pq(Glom_otu,
  rank_color = "Family",
  min_nb_seq = 1000
)

# For taxonomic comparison analysis with mock communities:
# 1. First prepare your data with fake taxa
physeq_with_fake <- add_shuffle_seq_pq(Glom_otu, nb_seq_fake = 50)

# 2. Perform taxonomic assignment (using your preferred method)
# 3. Compare results against known taxonomy
# tc_metrics_mock(physeq_with_fake, ranks_df, true_values_df)

Documentation

Package website: https://adrientaudiere.github.io/comparpq/
Getting started vignette: See the package vignettes for comprehensive examples
Function documentation: All functions have detailed help pages accessible via ?function_name

This package extends the functionality of: - {MiscMetabar}: Miscellaneous functions for metabarcoding analysis - {phyloseq}: Handling and analysis of high-throughput microbiome census data

Citation

If you use comparpq in your research, please cite:

citation("comparpq")

License

GPL (>= 3)

Issues and Contributions

Please report bugs and feature requests at https://github.com/adrientaudiere/comparpq/issues

Author

Adrien Taudière (aut, cre, cph)
ORCID: 0000-0003-1088-1182
Email: adrien.taudiere@zaclys.net

comparpq