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Changelog

Source: NEWS.md

microEDA 1.0.1

Improvements

  • show_filter_history() and filter_features() now use the term “features” instead of “taxa”. This change more accurately reflects that rows may represent ASVs or OTUs that lack formal taxonomic classification.

microEDA 1.0.0

  • First official stable release on GitHub.
  • Package is feature-complete for the initial release cycle.

Features

Core Functionality

  • microEDA-class: Extends the phyloseq-class to store additional metadata and analysis history.
  • microEDA-class summarisation: show(), summary(), and show_filter_history() print overviews of microEDA objects to the console.
  • MetaPhlAn support: Load and merge MetaPhlAn profiles using load_metaphlan() and join_mpa_profiles().
  • Feature filtering: filter_features() filters taxa by abundance and prevalence, supporting both global and stratified (group-wise) operations.
  • Taxonomic agglomeration: agglomerate_taxa() aggregates taxa at specified ranks; a vectorized, faster alternative to phyloseq::tax_glom().
  • Taxonomy table utilities: Functions to trim or add taxonomic prefixes (e.g., k__, p__) in a taxonomyTable.
  • Conversion to phyloseq: to_phyloseq() converts metaphlanProfile and microEDA objects into standard phyloseq objects.
  • Taxonomic consistency check: check_taxonomic_consistency() identifies inconsistencies within a taxonomyTable.
  • Presence lists: get_presence_list() returns unique taxa present in each group defined by a sample metadata variable.
  • Taxa overlap analysis: get_taxa_overlaps() computes overlaps and unique sets of taxa across sample groups, serving as a programmatic alternative to UpSet plots.

Visualization Functions

microEDA provides a collection of ggplot2-based plotting functions for exploratory data analysis:

  • plot_taxa_barchart(): Visualizes taxonomic abundance across samples, supporting aggregation at any rank and grouping by metadata.
  • plot_taxa_heatmap(): Displays mean abundance and prevalence (detection frequency) of taxa within groups.
  • plot_taxa_upset(): Visualizes shared and unique taxa across multiple sample groups (complemented by get_taxa_overlaps()).
  • plot_taxa_sankey(): Illustrates hierarchical taxonomic relationships and abundance flow from higher to lower ranks.