Function to add a new optimization to an acmap object, with specified values.

addOptimization(
  map,
  ag_coords = NULL,
  sr_coords = NULL,
  number_of_dimensions = NULL,
  minimum_column_basis = "none",
  fixed_column_bases = NULL,
  ag_reactivity_adjustments = NULL
)

Arguments

map

The acmap data object

ag_coords

Antigen coordinates for the new optimization (0 if not specified)

sr_coords

Sera coordinates for the new optimization (0 if not specified)

number_of_dimensions

The number of dimensions of the new optimization

minimum_column_basis

The minimum column basis to use for the new optimization

fixed_column_bases

A vector of fixed column bases with NA for sera where the minimum column basis should be applied

ag_reactivity_adjustments

A vector of antigen reactivity adjustments to apply to each antigen. Corresponding antigen titers will be adjusted by these amounts when calculating column bases and table distances.

Value

Returns the acmap data object with new optimization added (but not selected).

See also