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S7 class for comparing phyloseq objects

Source: R/list_phyloseq.R
list_phyloseq.Rd

lifecycle-experimental

A class to store and compare multiple phyloseq objects. It contains:

  • A list of phyloseq objects

  • A summary table with computed characteristics for each phyloseq

  • A list of comparison characteristics between phyloseq objects

An S7 class to store and compare multiple phyloseq objects.

Usage

list_phyloseq(
  physeq_list,
  names = NULL,
  same_primer_seq_tech = TRUE,
  same_bioinfo_pipeline = TRUE
)

Arguments

physeq_list

(required) A named list of phyloseq objects.

names

(character vector, default NULL) Optional names for the phyloseq objects. If NULL and the list is unnamed, names are generated automatically.

same_primer_seq_tech

(logical, default TRUE) Whether the same primer and sequencing technology was used across all phyloseq objects. Set to FALSE when comparing different primers (e.g., ITS1 vs ITS2) or technologies (e.g., Illumina vs PacBio).

same_bioinfo_pipeline

(logical, default TRUE) Whether the same bioinformatics pipeline was used across all phyloseq objects. Set to FALSE when comparing different clustering methods, taxonomic databases, or analysis parameters.

Details

lifecycle-experimental

The combination of same_primer_seq_tech and same_bioinfo_pipeline along with detected sample overlap determines the comparison type:

same_samplessame_primer_seq_techsame_bioinfo_pipelineType
TRUETRUETRUEREPRODUCIBILITY
TRUETRUEFALSEROBUSTNESS
TRUEFALSE-REPLICABILITY
nested--NESTED_ROBUSTNESS
FALSE--EXPLORATION or SEPARATE_ANALYSIS

Slots

phyloseq_list

A named list of phyloseq objects

summary_table

A tibble summarizing each phyloseq object

comparison

A list of characteristics comparing the phyloseq objects

Types of Comparison

The list_phyloseq class determines the type of comparison based on:

  • Detected characteristics (sample overlap, nested samples, shared modalities)

  • User-provided parameters (same_primer_seq_tech and same_bioinfo_pipeline)

There are six main types of comparisons:

REPRODUCIBILITY

Same pipeline (same_bioinfo_pipeline = TRUE), same primer/technology (same_primer_seq_tech = TRUE), same samples. Used to test reproducibility of results when running the exact same analysis multiple times.

ROBUSTNESS

Different pipeline (same_bioinfo_pipeline = FALSE, e.g., different clustering method, different assignment database) but same primer/technology (same_primer_seq_tech = TRUE), same samples. Used to test robustness of conclusions to methodological choices.

NESTED_ROBUSTNESS

One phyloseq object is derived from another, with samples being a subset (e.g., rarefied version created with rarefy_even_depth()). Used to test robustness to data processing choices like rarefaction, filtering, or subsetting. Comparisons should focus on the common (nested) samples.

REPLICABILITY

Different primer and/or technology (same_primer_seq_tech = FALSE, e.g., ITS1 vs ITS2, Illumina vs PacBio), same samples. Used to test replicability across taxonomic groups or sequencing technologies.

EXPLORATION

Different samples but with shared modalities. Useful to explore differences among groups of samples. Note: consider merging samples into one phyloseq object for some analyses instead.

SEPARATE_ANALYSIS

Different samples with no shared modalities. Separate analysis of each phyloseq object is recommended as direct comparison may not be meaningful.

Examples

# REPRODUCIBILITY: Same samples, same pipeline (default)
lpq_repro <- list_phyloseq(list(run1 = data_fungi, run2 = data_fungi))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: REPRODUCIBILITY
#> ℹ 185 common samples, 1420 common taxa
#> ✔ list_phyloseq created (REPRODUCIBILITY)

# ROBUSTNESS: Same samples, different pipeline
lpq_robust <- list_phyloseq(
  list(method_A = data_fungi, method_B = data_fungi),
  same_bioinfo_pipeline = FALSE
)
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: ROBUSTNESS
#> ℹ 185 common samples, 1420 common taxa
#> ✔ list_phyloseq created (ROBUSTNESS)

# REPLICABILITY: Same samples, different primer/technology
lpq_replic <- list_phyloseq(
  list(ITS1 = data_fungi, ITS2 = data_fungi),
  same_primer_seq_tech = FALSE
)
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: REPLICABILITY
#> ℹ 185 common samples, 1420 common taxa
#> ✔ list_phyloseq created (REPLICABILITY)