Figure repo for Engemann et al 2020 brain age paper.
Making the figures requires a:
- the (non-committed)
./data
directory (obtained from the authors) - a recent Python install including (>=3.5), ideally Anaconda, with Pandas. For details, see file: 'python_requirements.txt'
- ideally, a recent R Version (>= 3.0).
I did my best to keep the R dependencies flat, avoiding the tidyverse and other meta-packages. All logic and control flow is written in conservative base R and avoids pipe operators and other high-level syntax. The following visualization packages are needed to run the code in a pure R console:
To build the Markdown and HTML, you will also need:
The dependencies themselves have rather flat dependencies. Ggplot, may depend on a few elements of the tidyverse. However, running the code here should be possible with a rather minimalistic R setup.
The figure elements are created through R scripts, which at the same time implement elements of literate programming through RMarkdown directives.
The prinicipal R scripts begin follow the figure_*.r
pattern and can be
run in the R console or can be compiled through Rmarkdown into HTML outputs.
In both cases, the figure elements are created and written to ./figures
.
To build the figures together with the HTML, please consider the Makefile. You can build a single figure:
make fig2
Or all figures:
make all