phyloseq

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.56.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: ade4, ape, Biobase, BiocGenerics, biomformat, Biostrings, cluster, data.table, foreach, ggplot2, igraph, multtest, plyr, reshape2, scales, vegan
• Install: BiocManager::install("phyloseq")

When to Use

• Importing and storing complex phylogenetic sequencing data (OTU tables, sample metadata, taxonomy, trees) into a single object using import().
• Estimating and visualizing alpha diversity using plot_richness() with measures like "Chao1" or "Shannon".
• Performing beta diversity ordination (e.g., PCoA, NMDS, CCA) using ordinate() and visualizing the results with plot_ordination().
• Creating exploratory bar plots of taxonomic abundance across samples using plot_bar().

When NOT to Use

• For advanced network analysis beyond basic ecological similarity, use igraph directly because plot_net() provides only a default Jaccard co-occurrence network.
• For complex custom plotting beyond standard wrappers, use ggplot2 directly because phyloseq wrappers are built on it but may restrict advanced geoms.

Data Requirements

• Pre-clustered phylogenetic sequencing data (OTU/ASV table).
• Associated sample data (metadata), a phylogenetic tree, and/or taxonomic assignments.
• Raw (untrimmed) OTU-clustered data is strictly required when performing richness estimates.