Code for Smith et al 2019

Genetics of shoot branching plasticity in Brachypodium dystachion

Contains code to reproduce analysis of the paper.

Open RStudio project (BrachyRILs.Rproj file), and define all paths relative to the root directory of the project.

Directory structure:

project
├── data                - this will eventually live in an external repository
│   ├── external        - data from external sources (e.g. RIL genotypes)
│   ├── intermediate    - intermediate data that we may not need to share
│   ├── processed       - processed (clean) data that we might want to share
│   └── raw             - original, uncleaned, data (CSV format)
├── figures             - pdf files with figures generated by respective scripts
├── notebooks           - Rmarkdown documents with exploratory analysis
└── scripts             - R scripts with core analysis
    ├── data_processing - to process data, e.g. raw -> clean phenotypes
    ├── model_fitting   - to fit models (e.g. QTL and GxE models)
    └── paper_figures   - to create paper figures

Script naming conventions:

• Notebooks: person initials, 2-digit number, short description, e.g. ht-01_explore_qtl_models.Rmd, mvr-01_explore_phenotypes.Rmd
  • these can be knitted as html in the same directory
• Data processing scripts: 2-digit number, short description, e.g. 01_clean_phenotypes.R, 02_summarise_phenotypes.R
• figures scripts: figure number using two digits, and appending "S" for supplementary, e.g.: Fig01.R, Fig02.R, S01Fig.R
  • these should output a PDF file named Fig01.pdf, etc. to the ./figures/ folder.
  • these might later be processed in inkscape or illustrator.
• model_fitting scripts: 2-digit number, short description, e.g. 01_GxE_phenotype_lmm.R, 02_simple_qtl.R, 03_GxE_qtl.R