This repository contains the code and output for the paper by Netzl et al. Please cite the original publication if any data or code from this repository is used.
The repository's DOI was created with Zenodo (https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)
All data and metadata can be found in the data directory. The raw data is a local copy of this google sheet and stored in the data/google_sheet_tables directory.
The forest plots in Figure 1 and supplementary Figure is created with the code/plotting/forest_plots.R script.
The code/plotting/fold_change_over_time_cumulative.R creates Figure 2. This script also creates Table 1, stored in data/summary_tables.
The code/plotting/data_since_exposure.R creates the supplementary Figure showing titers and fold changes over time since exposure.
The code/cartography directory contains the scripts to create and plot antigenic maps, antibody landscapes and perform map diagnostics. The first script to run is create_titer_table.R, which stores titer tables in data/titer_tables, followed by map_creation.R to create the base maps. The maps are save in data/maps. The comparison map data/maps/roessler_et_al2023.ace was originally published in Rössler, Netzl, et al. Nat Commun 14, 5224 (2023) (https://doi.org/10.1038/s41467-023-41049-4)
and the Wilks_et_al_map_ndsubset_no_outliers_slope_adjusted.ace map in Wilks, Mühlemann, et al., Science (2023) (https://doi.org/10.1126/science.adj0070).
Table 2 is created in the code/summary_tables/gmt_fc_table_updated.R script. This directory contains other scripts to generate the supplementary tables. All tables are stored in the data/summary_tables directory.
In general, output figures are stored in the figure directory, tables in data/summary_tables.
All analyses were performed in R version 4.2.2 (2022-10-31). R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Antigenic maps were constructed using the Racmacs package, Version 1.1.35: Wilks S (2022). Racmacs: R Antigenic Cartography Macros. https://acorg.github.io/Racmacs, https://github.com/acorg/Racmacs.
Antibody landscapes were constructed using the ablandscapes package, Version 1.1.0: Wilks S (2021). ablandscapes: Making Antibody landscapes Using R. R package version 1.1.0, https://github.com/acorg/ablandscapes.