Data and analysis code for a toxin induction study on two species of Dinophysis dinoflagellates

General description

This repository contains the datasets, analysis code and output generated and used in the manuscript "Effects of copepod chemical cues on intra- and extracellular toxins in two species of Dinophysis", which has been published as a research article in Harmful Algae (https://doi.org/10.1016/j.hal.2024.102793).

Files

HRMS_data_Dinophysis_induction_experiment.zip contains the source high-resolution mass-spectroscopy endometabolomics data in open file formats.

Put_annot_sign_affect_feat_metabol_data.xlsx (corresponds to Supplementary spreadsheet 1 in the main manuscript) contains putative annotations of significantly affected features from the metabolomics data, for each Dinophysis species (D. sacculus and D. acuminata) and each mode of ionization. Notably, results obtained from GNPS (Global Natural Products Social Molecular Networking, https://gnps.ucsd.edu/), and SIRIUS (https://bio.informatik.uni-jena.de/sirius/) were mentionned. When available, MS/MS spectra were also provided. 

Tabl_sign_affect_feat.xlsx (corresponds to Supplementary spreadsheet 3 in the main manuscript) contains tables of significantly affected features (ANOVA, Tukey’s post hoc test, adjusted p-value cut-offs of 0.001 or 0.01) from the metabolomics data, for each Dinophysis species (sacculus and acuminata) and each mode of ionization. A visual representation (heatmaps) of these significant fetures are available as Figs S3-S6 in the supplementary information of the main mauscript. 

Toxin_analysis_code_output.Rmd is the R-markdown file that produces the interactive analysis output output (Toxin_analysis_code_output.html, corresponds to Supplementary code & output in the main manuscript) of the toxin analysis, and uses the datasets Toxin_analysis_data.csv,  pca_score_sacculus.csv, and pca_score_acuminata.csv source datasets to perform the statistical analyses and generate figures (details for each dataset below).

Toxin_analysis_data.csv (corresponds to Supplementary spreadsheet 2 in the main manuscript) contains the main data used to statistically analyse the toxin and growth dynamics of both Dinophysis species in response to different grazer treatments, and to produce the majority of the figures in the main manuscript (Figs. 2-6) and supplementary information (Figs. S1-S2). 

pca_score_sacculus.csv & pca_score_acuminata.csv contain the scores of the first two principal components of the PCA performed on LC-HRMS derived metabolomic profiles of D. sacculus and D. acuminata respectively, in both positive and negative ion mode. These are used to produce PCA score plots (Fig. 6 in the main manuscript and Fig. S2 in the supplementary information).

custom.css is a custom html style sheet file that formats the Toxin_analysis_code_output.html to display scrollable tables correctly. It is used by Toxin_analysis_code_output.Rmd and is necessary for true reproduction of the output (.html) file.