The Source Data and the code for reproducing the figures in TaxVAMB paper.
data folder contains all the necessary Source Data.
Most of the figures of the paper are made in Python and can be reproduced by running the Jupyter notebook scripts_python/Figures.ipynb.
pip install -r requirements.txt
jupyter notebook
The trees from Figure 4c, Figure 6a and Supplementary Figure 8 are made in R. The Figure 4c for instance only requires the summary and the tree that is an output of GTDBtk (v220 here, so gtdbtk.bac120.summary.tsv and gtdbtk.backbone.bac120.classify.tree).
Rscript scripts_R/Figure4c.R --tree data/human_longread.tree --summary data/human_longread_summary.tsv --output figures/figure4c_human_gut.pdf
Rscript scripts_R/Figure4c.R --tree data/sludge.tree --summary data/sludge_summary.tsv --output figures/figure4c_sludge.pdf
Rscript scripts_R/Figure6a.R
Rscript scripts_R/Supplementary_Figure8.R
The figures will appear in the figures folder.