topolow (version 1.0.0)

create_and_optimize_RACMACS_map: Create and Optimize a RACMACS Map

Description

Creates and optimizes an antigenic map using the RACMACS package and keeps the best optimization result. This function wraps common RACMACS functionality to provide a simplified interface for map creation and optimization.

Usage

create_and_optimize_RACMACS_map(
  titer_table,
  dim = 2,
  optimization_number = 400,
  output_file = NULL,
  num_cores = 1
)

Value

A racmap object from the Racmacs package, containing the optimized coordinates and other map data.

Arguments

titer_table

Matrix or data frame of titer measurements.

dim

Integer number of dimensions for the map (default: 2).

optimization_number

Integer number of optimization runs (default: 400).

output_file

Character. An optional, full path (including filename and extension) where the map coordinates will be saved as a CSV file. If NULL (the default), the coordinates are not saved to a file.

num_cores

Integer number of cores to use for parallel optimization (default: 1).

Examples

# Create a dummy titer table for the example
ag_names <- paste("V", 1:5)
sr_names <- paste("S", 1:4)
titer_table <- matrix(
  sample(c(10, 20, 40, 80, 160, 320, 640, 1280, 2560, 5120), 20, replace = TRUE),
  nrow = length(ag_names), ncol = length(sr_names),
  dimnames = list(ag_names, sr_names)
)

# Create and optimize map without saving coordinates
map_obj <- create_and_optimize_RACMACS_map(titer_table)

# Create map and save coordinates to a temporary file.
# tempfile() creates a path in the session's temporary directory.
temp_coords_file <- tempfile(fileext = ".csv")
map_obj_saved <- create_and_optimize_RACMACS_map(
  titer_table, 
  dim = 3,
  optimization_number = 100,
  output_file = temp_coords_file
)

# Check that the file was created
file.exists(temp_coords_file)

# Clean up the temporary file
unlink(temp_coords_file)