microEDA

Overview

R package for microbiome exploratory data analysis. Currently under active development.

Installation

You can install the development version of microEDA from GitHub with:

# install.packages("pak")
pak::pak("jrotzetter/microEDA")

Or the remotes package:

# install.packages("remotes")
remotes::install_github("jrotzetter/microEDA", build_vignettes = TRUE)

Currently implemented features

• microEDA() class extending phyloseq to hold additional information.
• Load and join MetaPhlAn profiles with load_metaphlan() and join_mpa_profiles().
• filter_features() by abundance and prevalence. Filtering can be applied globally or within groups (stratified) defined by a metadata variable.
• Aggregate taxa of the same taxonomy at specific taxonomic ranks with agglomerate_taxa(). This implementation is significantly faster than phyloseq::tax_glom.
• Functions to easily trim or add taxonomic prefixes to a taxonomyTable.
• to_phyloseq() to convert metaphlanProfile and microEDA objects into a phyloseq object.
• Check for taxonomic inconsistencies within a taxonomyTable with check_taxonomic_consistency()

Planned features

microEDA is planned to provide a collection of plotting functions, built on ggplot2, and designed for exploratory analysis of microbiome data.

1. Taxonomic Composition Barplot
   • Visualize the relative abundance of taxa within samples
   • Aggregate data at any taxonomic rank (e.g., Phylum, Genus)
   • Group samples by metadata variables (e.g., treatment, disease state)
   • Custom color palette to increase available distinct colors is planned
2. Mean Abundance & Prevalence Heatmap Table
   • Each cell will display:
     • Mean Relative Abundance of a taxon within a group
     • Prevalence indicating the proportion of samples within a group where a taxon is detected
   • This combined view helps distinguish between consistently abundant taxa and those that are highly variable
3. Taxonomic Intersection UpSet Plot
   • Show the number of shared and unique taxa between any number of sample groups
   • Separate function to obtain list of intersections will be provided
4. Taxonomic Flow Sankey Plot
   • Visualize the hierarchical relationship from higher (e.g., Phylum) to lower (e.g., Species) taxonomic ranks
   • Either plot the relative abundance “flow” for a single sample or the mean abundance across a group of samples