This repository contains the minimal dataset and code required to reproduce most of the figures in our Nature Communications pulbication. The code is licensed under GPL v3. The data is made available in the interests of transparency, but please discuss with us if you wish to use these data for another project.
The main file is clarity_figures.Rmd which is an Rmarkdown file. This requires the following packages and their dependencies to be installed from CRAN:
- rmarkdown
- purrr
- ggplot2
- dplyr
- readr
- forcats
- tidyr
- stringr
- ggbeeswarm
- forestmodel
- cowplot
- survminer
- lme4
- lmerTest
Once these are installed, the file can be rendered using rmarkdown::render("clarity_figures.Rmd) or
from within RStudio.
renv is used for package management.