Package index • comparpq

list_phyloseq Class

S7 class for storing and comparing multiple phyloseq objects

Functions for comparing phyloseq objects at a fine-grained level

Functions for manipulating list_phyloseq objects

add_phyloseq(): Add a phyloseq object to a list_phyloseq
apply_to_lpq(): Apply a function to all phyloseq objects in a list_phyloseq
filter_common_lpq(): Filter phyloseq objects to keep only shared samples and/or taxa
merge_lpq(): Merge a list_phyloseq into a single phyloseq object
n_levels_lpq(): Count unique taxonomic levels across phyloseq objects
remove_phyloseq(): Remove a phyloseq object from a list_phyloseq
shared_mod_lpq(): Display shared sample_data modalities
update_list_phyloseq(): Update the summary table and comparison characteristics

Visualization functions for list_phyloseq objects

formattable_lpq(): Formattable visualization for list_phyloseq summary
formattable_lpq_full(): Extended formattable for list_phyloseq with comparison info
gg_hill_lpq(): Scatter plots of Hill diversity across pairs of phyloseq objects
upset_lpq(): UpSet or Venn plot of shared taxonomic values across phyloseq objects

Statistical analysis functions for list_phyloseq objects

adonis_lpq(): PERMANOVA analysis on each phyloseq object in a list_phyloseq
aldex_lpq(): ALDEx2 analysis on each phyloseq object in a list_phyloseq
ancombc_lpq(): ANCOM-BC analysis on each phyloseq object in a list_phyloseq
estim_cor_lpq(): Estimation statistics for numeric correlation on a list_phyloseq
estim_cor_pq(): Estimation statistics for numeric variable correlation on a phyloseq object
estim_diff_lpq(): Estimation statistics for categorical comparisons on a list_phyloseq
estim_diff_pq(): Estimation statistics for categorical comparisons on a phyloseq object
gg_aldex_plot(): ggplot2 version of ALDEx2 diagnostic plots
gg_maaslin3_plot(): Plot MaAsLin3 results
glmulti_lpq(): Automated model selection for Hill diversity on each phyloseq in a list_phyloseq
maaslin3_pq(): Run MaAsLin3 differential abundance analysis on a phyloseq object
multipatt_lpq(): Indicator species analysis on each phyloseq object in a list_phyloseq

Functions for utilities on taxonomic data

Functions for computing accuracy metrics comparing taxonomic assignments

tc_congruence_metrics(): Compute congruence metrics between two taxonomic assignments
tc_metrics_mock(): Compute accuracy metrics of multiple taxonomic assignations method using mock for multi-rank and multi assignation methods
tc_metrics_mock_vec(): Compute accuracy metrics of taxonomic assignation using a mock (known) community for one rank

Visualization functions for comparing taxonomic assignments

Interactive plotting functions for phyloseq objects

bubbles_pq(): Bubble plot of phyloseq object with observablehq
gg_bubbles_pq(): Circle-packed bubble plot of a phyloseq object using ggplot2

Functions for adding fake taxa to test taxonomic assignment accuracy

add_external_seq_pq(): Add external sequences to a phyloseq object
add_shuffle_seq_pq(): Add fake sequences by shuffling existing ones in a phyloseq object
midasim_pq(): Simulate microbiome data with differential abundance using MIDASim
multiply_counts_pq(): Multiply OTU counts conditionally based on sample metadata
permute_da_pq(): Simulate differential abundance by redistributing OTU counts

Functions for modifying the tax_table slot of phyloseq objects

resolve_taxo_conflict(): Resolve taxonomic conflict in the tax_table of a phyloseq object
select_ranks_pq(): Select taxonomic ranks in a phyloseq object
rename_ranks_pq(): Rename names of ranks in the tax_table slot of a phyloseq object
taxtab_replace_pattern_by_NA(): Replace taxonomic value with a given pattern by NA

Helper functions for formatting tables

Helper functions for miscellaneous tasks