roessler_netzl_etal2026

Code for the manuscript by Rössler, Netzl, et al. 2026.

Requirements

R version

R >= 4.1.0 is recommended.

CRAN packages

install.packages(c(
  "tidyverse",
  "ggplot2",
  "patchwork",
  "readxl",
  "lubridate",
  "stringr",
  "cowplot",
  "ggrepel",
  "htmlwidgets",
  "webshot2",
  "png",
  "grid",
  "gridExtra",
  "Rmisc",
  "plyr",
  "rstatix"
))

GitHub packages

The following packages are from the Antigenic Cartography group and must be installed via remotes:

install.packages("remotes")

remotes::install_github("acorg/Racmacs")
remotes::install_github("acorg/ablandscapes")
remotes::install_github("acorg/r3js")
remotes::install_github("acorg/meantiter")

Data

The data/ directory is not included in this repository. The scripts expect the following structure under data/:

data/
  maps/          # Antigenic maps (.ace files)
  titer_data/    # Neutralization and binding titer data
  metadata/      # Serum group color tables and other metadata

Repository structure

All scripts are run from the code/ directory, we recommend creating an Rproject to easily set the home directory to ../code. They should be run in numerical order, as later scripts depend on outputs (RDS files, CSV files) generated by earlier ones.

Main analysis scripts

Script	Description
01_make_nhp_map_BA3_in_BA1.R	Builds the NHP antigenic map including BA.3.2.2 titrations. Saves the map and diagnostic plots.
02_fit_nhp_vacc_landscapes.R	Fits antibody landscapes to NHP vaccine serum groups. Saves landscape fit objects as RDS.
03-fit_biorep_landscapes.R	Fits antibody landscapes to human biorep neutralization data. Saves landscape fit objects and titer tables as RDS/CSV.
04-plota_biorep_landscapes_plot.R	Visualizes biorep and NHP landscapes. Saves interactive landscape HTML widgets and static comparison plots.
05-fit_biorep_T_cell_data.R	Fits CD4 and CD8 T cell antibody landscapes. Saves landscape fit objects and plots for T cell data.
06-fit_biorep_binding_landscapes.R	Fits antibody landscapes to human biorep binding (Luminex) data. Saves landscape fit objects and titer tables as RDS/CSV.
07-plot_biorep_binding_landscapes_plot.R	Visualizes biorep binding landscapes. Saves interactive HTML widgets and static comparison plots.
08-plot_biorep_over_time.R	Plots biorep neutralization GMTs and fold-changes over time.

Supplementary analysis scripts

These scripts are also run from the code/som2026 directory. Figures are saved as output in the respective directory.

Script	Description
optimum_exploration/02_nhp_map_diagnostics.R	Diagnostic analysis of multiple map optimization runs: stress distribution and procrustes RMSD across optima.
nhp_multiexposure_model/2608_NHP_biorep_modelled_amt_landscapes.R	Models multi-exposure antibody landscapes by summing NHP single-vaccine GMT landscapes and comparing to human biorep data.

Shared functions

The functions/ directory contains helper functions sourced by the analysis scripts:

• excel_to_titertable_functions.R — reading titer data from Excel files
• map_functions.R — Racmacs map utilities and ggplot wrappers
• long_map_info.R — converting map objects to long-format data frames
• titer_lineplot_functions.R — titer line plot helpers
• sr_group_color_functions.R — serum group color assignment
• sams_landscape_functions.R — antibody landscape plotting utilities

Outputs

All figures from code are saved in the figures/ directory, supplementary figures are saved directly in the som subdirectory:

• Static plots: PNG files at 300 dpi
• Interactive 3D landscapes: HTML widgets (viewable in any browser)

AI assistance

This code was prepared for publication with assistance from Claude Sonnet 4.6 (Anthropic). The AI assisted with converting internal lab notebook scripts to standalone R scripts suitable for public sharing, including removing lab-specific rendering syntax, replacing inline plot display calls with ggsave()/htmlwidgets::saveWidget() file output, and writing this README.