An extension to {MiscMetabar} and {phyloseq} package to compare phyloseq object • 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 development version of comparpq from GitHub with:

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

Main Features

Compare phyloseq objects

list_phyloseq: S7 class for storing and comparing multiple phyloseq objects, with automatic detection of comparison type (REPRODUCIBILITY, ROBUSTNESS, NESTED_ROBUSTNESS, REPLICABILITY, EXPLORATION, SEPARATE_ANALYSIS)
compare_refseq(): Compare reference sequences between two phyloseq objects, identifying shared/unique ASVs by name and by DNA sequence content
filter_common_lpq(): Filter phyloseq objects to keep only shared samples and/or taxa
apply_to_lpq(): Apply any function to all phyloseq objects in a list_phyloseq

Statistical Analysis

adonis_lpq(): PERMANOVA analysis across multiple phyloseq objects
estim_diff_pq() & estim_diff_lpq(): Estimation statistics for categorical comparisons using bootstrap confidence intervals (via dabestr)
estim_cor_pq() & estim_cor_lpq(): Estimation statistics for continuous correlations with bootstrap confidence intervals
ancombc_lpq(), aldex_lpq(), multipatt_lpq(), maaslin3_pq(): Differential abundance analysis methods

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
tc_sankey(): Sankey diagrams for taxonomic rank relationships
tc_linked_trees(): Side-by-side linked taxonomy trees for comparing two assignments
tc_congruence_metrics(): Congruence metrics between two taxonomic assignments
rainplot_taxo_na(): Rain plots for visualizing NA patterns in taxonomic data
formattable_lpq() & formattable_lpq_full(): Formatted summary tables with color bars for list_phyloseq
upset_lpq(): UpSet plots for visualizing sample/taxa overlap across phyloseq objects
gg_aldex_plot() & gg_maaslin3_plot(): ggplot2-based visualizations for differential abundance results

Data Manipulation

Mock community preparation: add_external_seq_pq(), add_shuffle_seq_pq(), multiply_counts_pq(), permute_da_pq(), midasim_pq() for creating and manipulating fake taxa to benchmark taxonomic assignment or differential abundance methods
Taxonomic table utilities: rename_ranks_pq(), select_ranks_pq(), resolve_taxo_conflict(), taxtab_replace_pattern_by_NA()
Taxonomy to tree: taxo2tree() to build a phylogenetic tree from taxonomy table

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