Autofigures Demo
This document is a demonstration as to how to quickly regenerate all figures in the manuscript using the autofigures programme. This demo was tested on a Debian-based Linux distribution, but should work on MacOS and Windows with the Windows Subsytem for Linux.
0. Set-Up: Downloading code and data
The first step is to pull the code from GitHub
git clone https://github.com/Emad-COMBINE-lab/pllm-ppi-data-leakage.git
cd pllm-ppi-data-leakage
Next, download and decompress the data archive from Zenodo. The file is a tar archive compressed with Zstandard. The README.md file in the data folder contains some alternative ways to download the data.
Note: the compressed download is >14.5GiB, which will take some time to download and decompress to 44.5GiB.
cd data
# download the data.tar.zstd file here
tar -I zstd -xvf data.tar.zstd
1. Install dependencies
You can use pip or poetry to install dependencies, but I prefer uv.
Follow these instructions to install uv.
Next, update your local python environment by running
cd ../autofigures
uv sync
The figures use the Inter font, so you'll have to install that as well if you want the figures to look like they do in the manuscript.
2. Generate all the figures.
Next, we can regenerate all the figures using
uv run python -m autofigures run_all
This should take less than 45 minutes, and result in the following files in the out directory:
total 34M
-rw-r--r--. 1 jszym jszym 313K Apr 17 23:10 acc_by_length.svg
-rw-r--r--. 1 jszym jszym 79K Apr 17 23:10 concordance.svg
-rw-r--r--. 1 jszym jszym 48K Apr 17 23:10 kw_k_ndcg.svg
-rw-r--r--. 1 jszym jszym 214K Apr 17 23:10 kw_ndcg_markers.svg
-rw-r--r--. 1 jszym jszym 432K Apr 17 23:10 length_heatmap_dscript.svg
-rw-r--r--. 1 jszym jszym 450K Apr 17 23:10 length_heatmap_esm.svg
-rw-r--r--. 1 jszym jszym 436K Apr 17 23:10 length_heatmap_intrepppid.svg
-rw-r--r--. 1 jszym jszym 423K Apr 17 23:10 length_heatmap_pipr.svg
-rw-r--r--. 1 jszym jszym 447K Apr 17 23:10 length_heatmap_prose.svg
-rw-r--r--. 1 jszym jszym 450K Apr 17 23:10 length_heatmap_proteinbert.svg
-rw-r--r--. 1 jszym jszym 451K Apr 17 23:10 length_heatmap_prottrans_bert.svg
-rw-r--r--. 1 jszym jszym 457K Apr 17 23:10 length_heatmap_prottrans_t5.svg
-rw-r--r--. 1 jszym jszym 435K Apr 17 23:10 length_heatmap_rapppid.svg
-rw-r--r--. 1 jszym jszym 400K Apr 17 23:10 length_heatmap_richoux.svg
-rw-r--r--. 1 jszym jszym 15K Apr 17 23:10 length_heatmap_sizes.svg
-rw-r--r--. 1 jszym jszym 450K Apr 17 23:10 length_heatmap_sprint.svg
-rw-r--r--. 1 jszym jszym 443K Apr 17 23:10 length_heatmap_squeezeprot_sp_nonstrict.svg
-rw-r--r--. 1 jszym jszym 444K Apr 17 23:10 length_heatmap_squeezeprot_sp_strict.svg
-rw-r--r--. 1 jszym jszym 444K Apr 17 23:10 length_heatmap_squeezeprot_u50.svg
-rw-r--r--. 1 jszym jszym 282K Apr 17 23:10 length_histogram.svg
-rw-r--r--. 1 jszym jszym 365K Apr 17 23:10 mutation_esm.png
-rw-r--r--. 1 jszym jszym 384K Apr 17 23:10 mutation_prose.png
-rw-r--r--. 1 jszym jszym 413K Apr 17 23:10 mutation_proteinbert.png
-rw-r--r--. 1 jszym jszym 378K Apr 17 23:10 mutation_prottrans_bert.png
-rw-r--r--. 1 jszym jszym 331K Apr 17 23:10 mutation_prottrans_t5.png
-rw-r--r--. 1 jszym jszym 423K Apr 17 23:10 mutation_squeezeprot_sp_nonstrict.png
-rw-r--r--. 1 jszym jszym 393K Apr 17 23:10 mutation_squeezeprot_sp_strict.png
-rw-r--r--. 1 jszym jszym 355K Apr 17 23:10 mutation_squeezeprot_u50.png
-rw-r--r--. 1 jszym jszym 142K Apr 17 23:10 mutation.svg
-rw-r--r--. 1 jszym jszym 22M Apr 17 23:10 sars_cov2_breakdown.svg
-rw-r--r--. 1 jszym jszym 1.6M Apr 17 23:10 sars_cov2_roc_highlight.svg
-rw-r--r--. 1 jszym jszym 960K Apr 17 23:10 sars_cov2_roc.svg
-rw-r--r--. 1 jszym jszym 107K Apr 17 23:10 speed.svg
-rw-r--r--. 1 jszym jszym 43K Apr 17 23:10 strict_nonstrict.svg
These files are all the panels (or components of the panels) in the figure.
For example, speed.svg corresponds to Fig. 1b in the manuscript and looks like:
What next?
Check out the autofigures and Experiments tabs above to geenerate individual figures or run individual experiments.