tfbpmodeling_paper_figures

Publication figures for the tfbpmodeling yeast TF regulatory network paper.

Structure

R/              Figure scripts and shared helpers
data/           Serialized data objects (gitignored)
plots/          Output SVGs (gitignored)

The data/ directory stores the results from tfbpmodeling in data/vx.x.x, eg data/v1.1.0. The processed results are stored under the data freeze date and the processed results are stored under the datafreeze date and the tfbpmodeling version, eg data/20250805 and data/20250805/1.0.0. See R/prepare_input_data.R (note: this will not run because the database will not be up. However, all of the data that this produces is already stored in data, so there is no need) and R/prepare_results_data.R.

Notebooks and figure scripts

The notebook paper_figures.Rmd and chisqr.Rmd both produce figures that are used in the paper. With the virtual environment installed via reticulate (use requirements.txt), you can run each to produce all of the figures in plots/. You can also run the figure creation scripts individually. Scroll down to the bottom of each file in R/ for code that will run in the console to individually create a figure.