MetaTreeMap

MetaTreeMap visualizes phylogenetic trees from metagenomic samples using nested rectangles whose areas are proportional to read counts or percentages mapped to species' reference genomes to convey hierarchical taxonomic structure and read distribution.

Key Features:

• Nested-rectangle representation: Uses nested rectangles to represent phylogenetic tree structure where each rectangle corresponds to a species/node.
• Quantitative area mapping: Rectangle area is proportional to the number or percentage of reads mapped to each species' reference genome.
• Adjustable node metrics: Visual parameters can be adjusted based on quantities assigned to tree nodes such as read number or percentage.
• Hierarchical overview and drill-down: Provides both high-level overviews and the ability to inspect detailed portions of large trees containing hundreds or thousands of species.
• Multi-sample comparison: Supports comparative visualization across multiple metagenomic samples.

Scientific Applications:

• Metagenomic profiling: Visualize and interpret taxonomic composition of metagenomic datasets using mapped-read abundances.
• Species composition analysis: Identify relative abundances of species via area-proportional mapping to reads or percentages.
• Phylogenetic read-distribution analysis: Examine distribution of genetic material across branches of the phylogenetic tree.
• Comparative metagenomics: Compare species abundance patterns across multiple samples.
• Microbial ecology and evolutionary biology: Support analyses that require hierarchical taxonomic and abundance information.

Methodology:

Represents phylogenetic trees as nested rectangles (treemap) with rectangle areas proportional to mapped read counts or percentages per species and allows adjustment of visual parameters according to node-associated quantities such as read number or percentage.