create_and_optimize_RACMACS_map {topolow} | R Documentation |
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
)
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). |
Value
A racmap
object from the Racmacs
package, containing the optimized coordinates and other map data.
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)
[Package topolow version 1.0.0 Index]