phylobar

phylobar interactively links stacked barplots with taxonomic or phylogenetic hierarchies to enable multiresolution exploration of compositional omics data.

Key Features:

• Interactive Hierarchy Navigation: Users can collapse or expand subtrees to explore data at different taxonomic or phylogenetic resolutions.
• Linked Visualization: Stacked barplots are dynamically linked with overview hierarchies to reveal patterns hidden in static overviews.
• Interactive Color Customization: Color palettes can be painted interactively for visual annotation.
• Taxon Search: Specific taxa can be searched within the hierarchical structure.
• Export Capabilities: Views can be exported as vector graphics files.
• Notebook Integration: Interactive plots can be embedded within R Markdown or Quarto notebooks.

Scientific Applications:

• Microbiome Analysis: Identification of variations in taxonomic groups across different resolutions, including detection of rare taxa and shifts at finer taxonomic levels that static barplots obscure.
• Immune Cell Composition Studies: Analysis of cell type hierarchies, as demonstrated in COVID-19 patient case studies.
• General Omics Applications: Applicable to any omics data with hierarchical organization beyond microbiome data.

Methodology:

phylobar uses the htmlwidgets library to link interactive D3 visualizations with R.