Integrative volcano plot export runlog ===================================== This script imports MS-DIAL feature tables for each culture medium, harmonizes feature identifiers, and merges raw feature metadata with one-factor univariate statistics and PCA loadings. It parses pairwise post hoc comparisons, computes pairwise log2 fold-changes from log2-transformed peak areas using a medium-specific pseudocount, and adjusts pairwise p-values within each medium and contrast using the Benjamini-Hochberg procedure. It then generates integrative volcano-style plots for the S1 vs S2 and S3 vs S2 comparisons, with log2 fold-change on the x-axis, -log10 adjusted q-values on the y-axis, and PCA loading magnitude in the PC1-PC2 plane encoded as point size. Only annotated features exceeding both the significance and effect-size thresholds are labeled. Finally, the plots are exported as editable vector graphics to PowerPoint and a run log is written for reproducibility. ===================================== Date: 2026-03-31 10:35:35 Working directory: C:/Users/2025tm006/Desktop/Publie extraction chimique mycotox/Data treatment MT/Figure integrative R version: R version 4.5.3 (2026-03-11 ucrt) Packages: - officer: 0.7.3 - rvg: 0.4.1 - ggplot2: 4.0.2 - dplyr: 1.1.4 - purrr: 1.2.1 Plot settings: - x-axis: pairwise log2 fold-change computed on log2(area + pseudocount) - displayed contrasts: S1_vs_S2 and S3_vs_S2 - y-axis: -log10(BH-adjusted pairwise q-value) computed within each medium and contrast - point size: PCA loading magnitude in the PC1-PC2 plane - significance threshold: q < 0.05 - effect-size threshold: |log2FC| >= 1 - labels: only annotated features above both thresholds Per-medium summary: # A tibble: 4 × 7 medium n_points n_sig n_big_effect n_annotated_labels min_q max_q 1 CMA 541 120 313 20 1.78e- 8 1 2 CZA 445 71 306 3 1.28e-12 1 3 MEA 555 57 322 12 3.48e-11 1 4 PDA 375 97 236 18 5.20e- 3 0.997