Convert EDA analysis script to parametrized Quarto report

[jibarozzo]

Overview

Convert the existing R script R/002_eda_analysis.R into a parametrized Quarto report to improve reproducibility, documentation, and flexibility.

Current State

• Script performs exploratory data analysis for microbiome data
• Hard-coded file paths and parameters
• Limited documentation and visualization output
• No structured reporting format

Proposed Changes

1. Create Quarto Document Structure

• Convert to .qmd format with YAML header
• Add parameter definitions for:
  • Input file paths (phyloseq object, metadata)
  • Analysis thresholds (prevalence cutoffs, read count filters)
  • Visualization options (colors, themes, figure dimensions)
  • Output options (file formats, directories)

2. Parameterize Key Variables

params:
  physeq_file: "data/output/processed/sabr_2023_physeq_object.rda"
  prevalence_threshold: 0.5
  min_reads: 5000
  output_dir: "reports/eda_output"
  figure_width: 10
  figure_height: 8
  theme: "minimal"

3. Improve Documentation

• Add narrative text explaining each analysis section
• Include interpretation of results
• Add method descriptions and citations
• Provide clear figure captions

4. Enhance Visualizations

• Add consistent theming across plots
• Include interactive plots where appropriate
• Ensure all plots have proper titles, labels, and legends
• Add summary tables for key findings

5. Structure Sections

• Executive Summary
• Data Overview
• Read Count Analysis
• Coverage Analysis
• Prevalence & Core Microbiome
• Conclusions and Next Steps

6. Output Options

• Support multiple output formats (HTML, PDF, Word)
• Include option for self-contained reports
• Add table of contents and cross-references

Implementation Notes

• Maintain compatibility with existing data objects
• Ensure all dependencies are properly loaded
• Add error handling for missing files or parameters
• Include session information for reproducibility

This conversion will make the EDA analysis more accessible to collaborators and easier to adapt for future projects.

[jibarozzo]

Closed by #10