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metagenome-visualization

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Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and Python. Covers why an ordination/bar/diversity number is a modeling choice that can manufacture a result, the MetaPhlAn-percent-vs-Bracken-counts fork that decides everything, CLR/Aitchison vs Bray-Curtis, Hill numbers and why shotgun richness is a database readout, pairing PERMANOVA with betadisper, and the multi-tool differential-abundance consensus. Use when plotting taxonomic/functional profiles, computing alpha/beta diversity, running ordination/PERMANOVA, or testing differential abundance. For amplicon/QIIME2 stats see the microbiome category; for compositional theory see abundance-estimation.

When to use

• plotting taxonomic/functional profiles
• computing alpha/beta diversity
• running ordination/PERMANOVA
• testing differential abundance
• visualizing shotgun profiler tables
• generating community statistics

When not to use

• amplicon/QIIME2 stats
• compositional theory
• input generation
• generic plotting primitives
• absolute load estimation

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