Convert Racmacs Map to Pairwise Distance Matrix

This utility function converts the output of a fitted Racmacs map into a pairwise Euclidean distance matrix between all antigenic strains.

Usage

racmaps_map_to_distances(map)

Arguments

map

A fitted Racmacs map object, typically the result of a Racmacs optimization run. The map must contain 2D coordinates for each antigen (strain).

Value

A symmetric matrix of pairwise Euclidean distances between strains, with row and column names corresponding to strain names.

Details

This function extracts the 2D coordinates of antigens from the Racmacs map and computes Euclidean distances between all pairs. Only the lower triangle is explicitly computed, and the upper triangle is filled by symmetry.

Examples

if (FALSE) { # \dontrun{
  map <- Racmacs::read.acmap("my_map_file.ace")
  distance_matrix <- racmaps_map_to_distances(map)
  print(distance_matrix)
} # }