Beta Diversity¶

Beta diversity describes differences in community composition between samples. We use PERMANOVA to test whether sample groups differ significantly in community composition, and ADONIS for multi-factor models.

PERMANOVA¶

All Samples, Unweighted UniFrac

Unweighted UniFrac considers only presence/absence of lineages (not their relative abundance):

qiime diversity beta-group-significance \
  --i-distance-matrix core_metrics/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --m-metadata-column sample_type \
  --o-visualization core_metrics/unweighted_unifrac_sample_type_significance.qzv

PERMANOVA¶

All Samples, Weighted UniFrac

Weighted UniFrac accounts for the relative abundance of lineages:

qiime diversity beta-group-significance \
  --i-distance-matrix core_metrics/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --m-metadata-column sample_type \
  --o-visualization core_metrics/weighted_unifrac_sample_type_significance.qzv

ADONIS¶

Multi-Factor Test

ADONIS (permutational MANOVA) tests for the combined effects of multiple metadata variables:

qiime diversity adonis \

--i-distance-matrix core_metrics/weighted_unifrac_distance_matrix.qza \

--m-metadata-file metadata_q2_workshop.txt \

--o-visualization core_metrics/weighted_adonis.qzv \

--p-formula

The formula uses R-style additive notation: var1+var2+var3. For this dataset we want to test the combined effects of accumulated degree days (add_0c), facility, and sample type. Join them with + and no spaces.

--p-formula, R-style formula specifying which metadata columns to test. Additive effects: a+b+c. Interaction terms: a*b. Column names must match exactly what appears in your metadata file header.

Formula Syntax

The --p-formula argument uses R-style formula notation. add_0c+facility+sample_type tests the additive effects of accumulated degree days, facility, and sample type.

PERMANOVA¶

Soil Samples by Facility

First filter to soil samples and re-run core metrics (if not already done in the alpha diversity step):

qiime feature-table filter-samples \
  --i-table table_nomitochloro.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --p-where "[sample_type]='soil'" \
  --o-filtered-table table_nomitochloro_soil.qza

qiime diversity core-metrics-phylogenetic \
  --i-table table_nomitochloro_soil.qza \
  --i-phylogeny tree_gg2.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --p-sampling-depth 1500 \
  --output-dir core_metrics_soil

Test for facility effects within soil samples:

qiime diversity beta-group-significance \
  --i-distance-matrix core_metrics_soil/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --m-metadata-column facility \
  --o-visualization core_metrics_soil/unweighted_unifrac_facility_significance.qzv

Outputs¶

File	Type	Description
`core_metrics/unweighted_unifrac_sample_type_significance.qzv`	Visualization	PERMANOVA by sample type (unweighted)
`core_metrics/weighted_unifrac_sample_type_significance.qzv`	Visualization	PERMANOVA by sample type (weighted)
`core_metrics/weighted_adonis.qzv`	Visualization	ADONIS multi-factor model
`core_metrics_soil/unweighted_unifrac_facility_significance.qzv`	Visualization	PERMANOVA by facility (soil only)

Next: Differential Abundance (ANCOM-BC2)