This repository contains the code for the NHP antigenic cartography manuscript by Annika Rössler, Antonia Netzl, et. al., 2024. 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)
Raw data can be found in the data directory and will be added upon publication. The code for the analyses shown in the main manuscript can be found in the code directory. The alignment_map.ace in the data/maps directory is the human map from 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 is the human map from Wilks, Mühlemann, et al., Science (2023) (https://doi.org/10.1126/science.adj0070).
To obtain a titer table for antigenic map construction, execute the excel_to_titertable.R script. To construct maps, first the make_map_final.R script. Antibody landscapes are fit in the ablandscapes_fit_multi.R. The 3D_landscapes.Rmd creates an html script with 3D illustrations of the landscapes. The Bayesian titer comparison is done in the model_map_organism_assay_dataset_sigma.R script and plots are generated in the plot_stan_model_organism_assay.R. The STAN model is stored in the model directory.
The code for creating maps and titerplots can be found in the figure directory.
All SOM analyses can be found in the som directory, the Bayesian analysis SOM plots are generated in the scripts in the code directory.
Map diagnostics were performed using scripts in the map_diagnostics directory and as previously described in Rössler, Netzl, et al. Nat Commun 14, 5224 (2023) (https://doi.org/10.1038/s41467-023-41049-4).
The function directory contains utility functions, the data/metadata directory contains metadata such as colour information.
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.
Geometric mean titers and fold changes were calculated using the titertools package, Version 0.0.0.9001: Wilks SH (2022). titertools: A statistical toolkit for the annalysis of censored titration data. R package version 0.0.0.9001.
The Bayesian modelling was performed with cmdstanr: Gabry J, Češnovar R (2022). cmdstanr: R Interface to 'CmdStan'. https://mc-stan.org/cmdstanr/, https://discourse.mc-stan.org.