diversity¶
| Description |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata. |
|---|---|
| Version | 2024.5.1 |
| Website | https://github.com/qiime2/q2-diversity |
| Support |
Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org |
| q2cli Invocation | qiime diversity
|
| Artifact API Import | from qiime2.plugins import diversity
|
Pipelines¶
- alpha: Alpha diversity
- alpha-phylogenetic: Alpha diversity (phylogenetic)
- beta: Beta diversity
- beta-correlation: Beta diversity correlation
- beta-phylogenetic: Beta diversity (phylogenetic)
- core-metrics: Core diversity metrics (non-phylogenetic)
- core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)
Methods¶
- filter-alpha-diversity: Filter samples from an alpha diversity metric.
- filter-distance-matrix: Filter samples from a distance matrix.
- partial-procrustes: Partial Procrustes
- pcoa: Principal Coordinate Analysis
- pcoa-biplot: Principal Coordinate Analysis Biplot
- procrustes-analysis: Procrustes Analysis
- tsne: t-distributed stochastic neighbor embedding
- umap: Uniform Manifold Approximation and Projection
Visualizers¶
- adonis: adonis PERMANOVA test for beta group significance
- alpha-correlation: Alpha diversity correlation
- alpha-group-significance: Alpha diversity comparisons
- alpha-rarefaction: Alpha rarefaction curves
- beta-group-significance: Beta diversity group significance
- beta-rarefaction: Beta diversity rarefaction
- bioenv: bioenv
- mantel: Apply the Mantel test to two distance matrices