Reference

Merge samples or taxa

merge_samples2()

Merge samples by a sample variable or factor

merge_taxa_vec()

Merge taxa in groups (vectorized version)

tax_glom()

Agglomerate taxa using taxonomy.

tip_glom()

Agglomerate taxa using phylogeny-derived distances.

tree_glom()

Agglomerate taxa at a given phylogenetic resolution.

Transform or subset data

select_tax_table() select_sample_data()

Subset columns in the taxonomy table or sample data using their names and types

relocate_tax_table() relocate_sample_data()

Change column order in the taxonomy table or sample data

rename_tax_table() rename_with_tax_table() rename_sample_data() rename_with_sample_data()

Rename columns in the taxonomy table or sample data

filter_tax_table() filter_sample_data()

Subset rows in the taxonomy table or sample data using column values

mutate_tax_table() transmute_tax_table() mutate_sample_data() transmute_sample_data()

Create, modify, and delete columns in the taxonomy table or sample data

left_join_tax_table() left_join_sample_data() inner_join_tax_table() inner_join_sample_data()

Mutating joins of the taxonomy table or sample data

filter_taxa() filter_taxa2()

Filter taxa based on across-sample OTU abundance criteria

transform_sample_counts()

Transform abundance data in an otu_table, sample-by-sample

orient_taxa()

Orient a phyloseq object or otu table to have taxa as rows or as columns

Coercion

psmelt()

Melt phyloseq data object into large data.frame

as_tibble(<otu_table>) as_tibble(<sample_data>) as_tibble(<taxonomyTable>) as_tibble(<XStringSet>) as_tibble(<phyloseq>)

Coerce phyloseq objects to tibble data frames

otu_table(<tbl_df>) sample_data(<tbl_df>) tax_table(<tbl_df>)

Construct phyloseq objects from tibbles

Plotting

plot_bar()

A flexible, informative barplot phyloseq data

plot_heatmap()

Create an ecologically-organized heatmap using ggplot2 graphics

plot_tree()

Plot a phylogenetic tree with optional annotations

Other

unique_or_na()

Get the unique value in x or NA if none

show(<phyloseq>) show(<taxonomyTable>) show(<sample_data>) show(<otu_table>)

Methods for show() for phyloseq objects.