This repository contains all the materials and code for the analysis used in our final paper. Below is an overview of the contents and instructions on how to run the provided R scripts.
The final IMRaD report, detailing the statistical analysis, is available as a .html file in the docs folder. This report includes all statistical methodologies, results, and discussions pertinent to our study.
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raw-data: This folder contains the provided experimental data file
2024-03-05-WIF-tis4d.xlsx. It includes 88 observations with the following variables:cell_line: Type of cell line used (Wild-type or Cell-type 101).treatment: Treatment applied (Placebo or Activating Factor 42).name: Name of specific cell culture.conc: Concentration of growth factor.gene_expression: Resultant gene expression.
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data: This folder contains the processed and cleaned data (derived from the raw data).
- figs: This folder contains all figures saved as
.tifffiles. - tabs: This folder contains all tables saved as
.docxfiles.
- r-code: This folder contains all R scripts used for data processing, analysis, and visualisation.
To run any of the R scripts provided in the r-code folder, follow these steps:
- Open RStudio with the
.Rprojfile. - Ensure the project folder is set as the working directory. You can do this by using the
Sessionmenu in RStudio:Session -> Set Working Directory -> To Project Directory
- Locate and open the desired R script in the
r-codefolder. - Press Ctrl+Shift+S (or Cmd+Shift+S on macOS) to source and execute the script.
Upon execution, any relevant output will be printed to the console. Additionally, figures and tables will be generated and saved to the appropriate folders (figs and tabs, respectively).
Note: If you do not want to overwrite the original figures and tables, you may rename the file names used by gtsave() and ggsave() functions in the scripts.
For any questions, feel free to contact me at james.r.day@student.adelaide.edu.au.