Explorable Report

Assays Included in This Report

This report explicitly checks the hypothesis-suite inputs for WGS, 16S, and ITS. Included means nonzero sample and feature counts were loaded from the completed workflow exports.

Hypothesis Verdict Cards

Logical Steps

1. Step 1. Study Overview and QC
   Summarize assay coverage, sample inventory, control annotations, and high-level dataset structure.
   study_overview.tsv; metadata_column_catalog.tsv; hypotheses.imported.tsv
2. Step 2. Alpha Diversity
   Compute richness, Shannon, Simpson, evenness, and test them against targeted contrasts and every usable metadata column.
   diversity_metrics.tsv; diversity_tests.tsv; metadata_alpha_associations.tsv
3. Step 3. Beta Diversity and Community Structure
   Build Bray-Curtis dissimilarities, PCoA ordinations, and PERMANOVA summaries for assay-specific and metadata-driven effects.
   pcoa_coordinates.tsv; permanova.tsv; metadata_permanova.tsv; metadata_pcoa_associations.tsv
4. Step 4. Taxonomic Composition and Beneficial Taxa
   Screen for beneficial taxa, summarize source overlap, and prepare interpretable taxonomic summaries.
   beneficial_taxa_summary.tsv; source_overlap.tsv
5. Step 5. Differential Abundance and Function
   Test assay- and metadata-driven contrasts for taxonomic and WGS functional differences.
   differential_abundance.tsv; metadata_differential_abundance_summary.tsv; wgs_function_top_differences.tsv
6. Step 6. Core Microbiome and Cross-Assay Concordance
   Define core taxa, assess overlap across assays, and quantify assay bias or concordance on shared samples.
   core_taxa.tsv; cross_assay_sample_metrics.tsv; cross_assay_correlations.tsv
7. Step 7. Machine Learning and Network Structure
   Rank discriminatory features and summarize co-occurrence structure for hypothesis generation.
   random_forest_summary.tsv; random_forest_top_features.tsv; metadata_random_forest_summary.tsv; cooccurrence_network_edges.tsv
8. Step 8. Hypothesis Answer Layer
   Map outputs back to the stated hypotheses and surface the strongest metadata-linked signals.
   hypothesis_to_output_map.tsv; metadata_signal_summary.tsv; hypothesis_summary.md

Study Overview and QC

Metadata Catalog

QC Flags

QC Summary

Positive Control Evaluation

Positive Control Benchmark

Alpha Diversity

Alpha Metrics

Metadata-Wide Alpha Associations

Beta Diversity and Community Structure

Metadata PERMANOVA

No results produced.

Metadata Ordination Associations

No results produced.

Taxonomic Composition, Source Overlap, and Core Taxa

Core Taxa

Differential Abundance and Functional Contrasts

Differential Abundance

No results produced.

Metadata Differential Summary

No results produced.

Machine Learning and Metadata Signal Prioritization

Random Forest Top Features

No results produced.

Metadata Random Forest

No results produced.

Metadata Signal Summary

Metadata Covariate Links

Hypothesis Answer Layer

Hypothesis to Output Map

Markdown Summary

# GREENWALL Hypothesis-Oriented Analysis Summary

This report is organized as a logical analysis sequence modeled on a publication-style microbiome report.

## Executive Summary

- Imported hypotheses: 9
- Manifest samples: 57
- Metadata columns scanned: 20
- Metadata-linked signals at q < 0.1: 46

## Hypothesis Verdict Cards

- **Mixed**: Are there differences in 16S / WGS / ITS outcomes
  Evidence: Top metadata-linked signals were WGS:Accumulation Time (Days); WGS:Date Deployed; WGS:Days Deploy_to_Collect. 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; metadata_covariate_links.tsv; metadata_signal_summary.tsv; positive_control_benchmark.tsv
- **Mixed**: Are the collection of microorganisms found in the greenwall related to human health in any way?
  Evidence: 5 beneficial-taxa keyword hits were detected across assays. 2 positive-control benchmark summaries were generated.
  Outputs: beneficial_taxa_summary.tsv; core_taxa.tsv; hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Mixed**: Is the microbiome of the "greenwall room" different from the other airstreams?
  Evidence: Maximum source-overlap fraction observed was 0.797. 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv; source_overlap.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Mixed**: Is there evidence of diversification of the "greenwall room" microbiome by greenwall  microorganisms?
  Evidence: 46 alpha-diversity metadata associations passed q < 0.1. 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; metadata_alpha_associations.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Mixed**: Is there evidence of metabolic function within the greenwall microbiome related to chemicals identified in relevant airstreams?
  Evidence: Maximum source-overlap fraction observed was 0.797. 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv; source_overlap.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv
- **Not Supported Yet**: 
  Evidence: 2 positive-control benchmark summaries were generated.
  Outputs: hypothesis_summary.md; hypothesis_to_output_map.tsv; positive_control_benchmark.tsv

## Logical Steps

1. **Study Overview and QC**
   - Purpose: Summarize assay coverage, sample inventory, control annotations, and high-level dataset structure.
   - Outputs: study_overview.tsv; metadata_column_catalog.tsv; hypotheses.imported.tsv
2. **Alpha Diversity**
   - Purpose: Compute richness, Shannon, Simpson, evenness, and test them against targeted contrasts and every usable metadata column.
   - Outputs: diversity_metrics.tsv; diversity_tests.tsv; metadata_alpha_associations.tsv
3. **Beta Diversity and Community Structure**
   - Purpose: Build Bray-Curtis dissimilarities, PCoA ordinations, and PERMANOVA summaries for assay-specific and metadata-driven effects.
   - Outputs: pcoa_coordinates.tsv; permanova.tsv; metadata_permanova.tsv; metadata_pcoa_associations.tsv
4. **Taxonomic Composition and Beneficial Taxa**
   - Purpose: Screen for beneficial taxa, summarize source overlap, and prepare interpretable taxonomic summaries.
   - Outputs: beneficial_taxa_summary.tsv; source_overlap.tsv
5. **Differential Abundance and Function**
   - Purpose: Test assay- and metadata-driven contrasts for taxonomic and WGS functional differences.
   - Outputs: differential_abundance.tsv; metadata_differential_abundance_summary.tsv; wgs_function_top_differences.tsv
6. **Core Microbiome and Cross-Assay Concordance**
   - Purpose: Define core taxa, assess overlap across assays, and quantify assay bias or concordance on shared samples.
   - Outputs: core_taxa.tsv; cross_assay_sample_metrics.tsv; cross_assay_correlations.tsv
7. **Machine Learning and Network Structure**
   - Purpose: Rank discriminatory features and summarize co-occurrence structure for hypothesis generation.
   - Outputs: random_forest_summary.tsv; random_forest_top_features.tsv; metadata_random_forest_summary.tsv; cooccurrence_network_edges.tsv
8. **Hypothesis Answer Layer**
   - Purpose: Map outputs back to the stated hypotheses and surface the strongest metadata-linked signals.
   - Outputs: hypothesis_to_output_map.tsv; metadata_signal_summary.tsv; hypothesis_summary.md

## Step 1. Study Overview and QC

- Manifest rows: 57
- Manifest columns: 30
- Testable metadata columns: 23
- QC flag rows: 57
- Samples with recommended exclusion: 0

## Step 2. Alpha Diversity

- Targeted contrasts: 8
- Metadata-wide alpha tests: 95
- Top metadata-linked alpha signals:
```tsv
assay	metadata_column	metadata_type	metric	test	n	n_groups	statistic	pvalue	effect_direction	qvalue
WGS	Sample Material	categorical	library_size	kruskal	51	5.0	35.361773624185375	3.9145866564586555e-07	PDMS|Filter|Rhizosphere|Leaf|Zymo Mock Community	3.718857323635723e-05
WGS	Sample Material	categorical	shannon	kruskal	51	5.0	29.97622549019607	4.949285909900996e-06	PDMS|Filter|Rhizosphere|Leaf|Zymo Mock Community	0.0001813813893402897
WGS	paired_negative_control	categorical	library_size	kruskal	56	9.0	38.641656575471494	5.727833347588096e-06	PSKB1|PWKB5|PWKB3|PWFBA|PWFBC	0.0001813813893402897
WGS	Sample Material	categorical	evenness	kruskal	51	5.0	24.740874811463073	5.671956757119998e-05	PDMS|Filter|Rhizosphere|Leaf|Zymo Mock Community	0.0011793428847587607
WGS	Date Deployed	date	library_size	spearman	57		-0.5038310692604261	6.458960756609466e-05	negative	0.0011793428847587607
```

## Step 3. Beta Diversity and Community Structure

- Assay-specific PERMANOVA rows: 0
- Metadata PERMANOVA rows: 0
- Ordination metadata tests: 0

## Step 4. Taxonomic Composition and Beneficial Taxa

- Beneficial taxa screen rows: 5
- Source overlap rows: 2
- Positive-control diagnostic rows: 4

## Step 5. Differential Abundance and Function

- Taxonomic differential abundance rows: 0
- Metadata differential summaries: 0
- WGS functional contrasts: 0

## Step 6. Core Microbiome and Cross-Assay Concordance

- Core taxa rows: 4
- Cross-assay correlation rows: 0

## Step 7. Machine Learning and Networks

- Primary Random Forest summaries: 0
- Metadata Random Forest summaries: 0

## Step 8. Hypothesis Answer Layer

- Highest-signal metadata fields across all assays/tests:
```tsv
assay	metadata_column	alpha_tests	alpha_significant_q_lt_0_1	composite_signal_score	top_related_metadata
WGS	Accumulation Time (Days)	5	5	10	Concentration/Filtration Step?:1.000; Days Deploy_to_Collect:1.000; Greenwall Surface Position:1.000
WGS	Date Deployed	5	5	10	Qubit ng/uL:0.747; ng/50uL:0.747; Date Extracted:0.566
WGS	Days Deploy_to_Collect	5	5	10	Greenwall Radial Distance:1.000; Accumulation Time (Days):1.000; Concentration/Filtration Step?:1.000
WGS	Relevant Kit Blank	5	5	10	Accumulation Time (Days):1.000; Concentration/Filtration Step?:1.000; Days Deploy_to_Collect:1.000
WGS	Sample Material	5	5	10	Accumulation Time (Days):1.000; Days Deploy_to_Collect:1.000; Concentration/Filtration Step?:0.980
WGS	paired_negative_control	5	5	10	Concentration/Filtration Step?:1.000; Days Deploy_to_Collect:1.000; Extraction Kit:1.000
WGS	paired_positive_control	5	5	10	Concentration/Filtration Step?:1.000; Extraction Kit:1.000; Relevant Kit Blank:1.000
WGS	Airstream	5	4	9	Concentration/Filtration Step?:0.583; paired_negative_control:0.483; Sample Material:0.480
WGS	Days Collect_to_Extract	5	3	8	Date Extracted:0.626; Qubit ng/uL:0.562; ng/50uL:0.562
WGS	Relevant Field Blank	5	2	7	paired_negative_control:1.000; Concentration/Filtration Step?:0.725; Sample Material:0.725
```
- Strongest metadata-metadata covariate links:
```tsv
metadata_column_a	metadata_type_a	metadata_column_b	metadata_type_b	test	association_strength	statistic	pvalue
Days Deploy_to_Collect	categorical	Greenwall Radial Distance	categorical	cramers_v	1.0000000000000002	1.0000000000000002	
Accumulation Time (Days)	categorical	Concentration/Filtration Step?	categorical	cramers_v	1.0	1.0	
Accumulation Time (Days)	categorical	Days Deploy_to_Collect	categorical	cramers_v	1.0	1.0	
Accumulation Time (Days)	categorical	Greenwall Surface Position	categorical	cramers_v	1.0	1.0	
Accumulation Time (Days)	categorical	Relevant Kit Blank	categorical	cramers_v	1.0	1.0	
Accumulation Time (Days)	categorical	Sample Material	categorical	cramers_v	1.0	1.0	
Concentration/Filtration Step?	categorical	Days Deploy_to_Collect	categorical	cramers_v	1.0	1.0	
Concentration/Filtration Step?	categorical	Relevant Kit Blank	categorical	cramers_v	1.0	1.0	
Concentration/Filtration Step?	categorical	paired_negative_control	categorical	cramers_v	1.0	1.0	
Concentration/Filtration Step?	categorical	paired_positive_control	categorical	cramers_v	1.0	1.0
```