visualization

name	visualization
description	Statistical visualization checklist for shotgun metagenomics across QC, taxonomy, function, and binning outputs. Use when: (1) Choosing alpha/beta and composition figure types, (2) Labeling figures by stage and method, (3) Pairing plots with MaAsLin2/LEfSe/microeco. For end-to-end R workflows prefer microeco. Route via research-analysis.
license	MIT
category	evaluation
tags	["visualization","diversity","statistics","figures","research-analysis"]
stage	report

Visualization and statistics (checklist)

Route via research-analysis. For modular R pipelines prefer microeco.

Rules

1. Label every figure with stage + method + database release
2. Inspect batch structure before biological group tests
3. Report normalization, rarefaction (if any), test, and multiple-testing correction
4. Do not plot bins as “high-quality genomes” before mag-qc / checkm2 filters
5. Prefer vector PDF/SVG for journal figures; keep scripts + seed for reproducibility

By stage

QC

• Read counts / Q-score summaries → often via multiqc
• Host-depletion fractions before/after KneadData

Taxonomic annotation (reads)

• Alpha diversity boxplots / rarefaction curves
• Beta PCoA / NMDS + distance heatmaps
• Taxon heatmaps and stacked bars (relative abundance)
• Differential taxa: maaslin2 (default multivariable) · lefse (classic LDA)

Functional annotation

• HUMAnN pathway / gene-family heatmaps
• eggNOG / AMR / element-cycling summary bars (presence ≠ activity)

Binning / genomes

• Accumulation vs sample effort
• Completeness–contamination scatter (checkm2)
• GTDB phylogeny with quality annotations
• Annotation overlaps (UpSet), AMR / defense heatmaps on MAGs

Pairing

Plot goal	Prefer
Full R exploration suite	microeco
Multivariable volcano / coefficients	maaslin2
Cladogram / LDA scores	lefse
Multi-sample QC HTML	multiqc

Related skills

research-analysis · microeco · maaslin2 · lefse · multiqc · metaphlan · kraken2 · humann · coverm · gtdbtk · basalt · mag-qc · anvio · tool-selection