Dataset for: Maximin model analysis reveals context dependent roles of P2K1/P2K2 in Arabidopsis root resource allocation

Description

This dataset supports a phenotype-level reanalysis of Arabidopsis thaliana wild type, p2k1, p2k2 and p2k1 p2k2 seedlings across seven nutrient, light and pH environments. The package contains the archived source phenotype workbook, a reorganized raw-data workbook, the 623-seedling analysis matrix, six root traits, all final model and statistical outputs, and the Python, R and JavaScript code used to reproduce the reported results. The long-format table contains 3,738 genotype-condition-trait records from 623 individual seedlings. No sequencing, transcriptomic, proteomic or metabolomic data were generated for this study. In the reorganized workbook, raw_data/Raw_Data.xlsx carries the 623-seedling and 3,738-record matrices together with the environment, genotype, trait and model definitions. Data and documentation are licensed under CC BY 4.0. Code is licensed under the MIT License.

Steps to reproduce

Run all commands from the dataset root directory. Python: python code/python/recompute_jpp_game_model.py python code/python/recompute_jpp_multivariate.py R: Rscript code/R/run_all_figures.R --refresh-data JavaScript figure route: node code/javascript/build_jpp_figures.mjs The Python and R analyses use bootstrap and permutation seed 20260928 and 5,000 replicates. Required packages and the software environment are listed in metadata/SOFTWARE_ENVIRONMENT.md. File integrity can be checked against checksums/SHA256SUMS.txt.

Institutions

• Northwest Normal University

  Gansu, Lanzhou

Categories

Licence