Mapping SARS-CoV-2 antigenic relationships and serological responses

This repository contains all the data and code for the paper "Mapping SARS-CoV-2 antigenic relationships and serological responses".

Viewing interactive figures

Interactive versions of each of the figures in the docs directory and are available here.

Running the code

Dependencies

Code package dependencies are listed in the DEPENDENCIES file.

titertools (v0.0.0.9002)

Several functions we use for a likelihood-based approach to dealing with censored titer data are included in the "titertools" package available at github.com/shwilks/titertools. Here we use version the package version 0.0.0.9002.

Racmacs (v1.2.3)

For performing antigenic cartography we use the "Racmacs" package v1.2.3, available from github.com/shwilks/Racmacs.

ablandscapes (v1.2.3)

For plotting antibody landscapes we use the "ablandscapes" package v1.1.2, available from github.com/shwilks/ablandscapes.

To reprocess the raw data and generate the data in data/generated_data run the file code/generate_data.R. Note that some of the map bootstrapping in particular may take a considerable amount of time to run.

To regenerate all figures run the file code/generate_figures.R.

To regenerate all interactive figures run the file code/generate_docs.R.

Directory structure

Directory	Description
code/figures	Code for figure generation
code/docs	Code for interactive figure generation in docs/
code/data_generation	Code for data processing
data/raw_data	Raw measurement data files
data/generated_data	Data generated after processing (for example data after model fits)
data/maps	Antigenic map data
docs	Interactive figure documents
figures	Generated figures
functions	Functions shared across code