| 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
- Label every figure with stage + method + database release
- Inspect batch structure before biological group tests
- Report normalization, rarefaction (if any), test, and multiple-testing correction
- Do not plot bins as “high-quality genomes” before
mag-qc / checkm2 filters
- 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
