chico_study_manuscript

Code and sanitized plotting data for the CHICO study manuscript project.

Main folders

• 1_code/: plotting scripts and code references
• 3_data_analysis/plot_data/: de-identified data used for plotting
• 3_data_analysis/figures/: generated figures

Code organization

• 1_code/00_plot_helpers.R: shared paths and figure export helpers
• 1_code/01_plot_taxonomy_tree.R: circular taxonomy tree
• 1_code/02_plot_genus_gam_edf_vs_fdr.R: genus GAM significance plots
• 1_code/03_plot_alpha_diversity_gam_curves.R: alpha-diversity GAM curves
• 1_code/04_plot_deswan_real_vs_permuted.R: DE-SWAN real versus permuted comparison
• 1_code/05_plot_deswan_repeat10_grid.R: repeat-10 DE-SWAN grid plot
• 1_code/06_plot_age_balance_bars.R: balanced age-bin bar plot
• 1_code/07_plot_lefse_genotype_upset.R: genotype-level LEfSe upset plots
• 1_code/original_from_hpv_project/: original plotting scripts copied from hpv_project for reference
• 1_code/plot_manifest.md: notes on what was migrated and what was intentionally excluded

Privacy

This repository keeps only plotting-level data needed to regenerate selected figures.

• Participant-level phenotype data were not copied here
• Sample-level microbiome abundance matrices were not copied here
• Only de-identified summary tables needed for plotting were placed in 3_data_analysis/plot_data/

Re-running plots

Open the RStudio project chico_study_manuscript.Rproj, then run the scripts in 1_code/.

All generated figures are written to:

• 3_data_analysis/figures/