addOptimization: Add a new optimization to an acmap object

In Racmacs: Antigenic Cartography Macros

Add a new optimization to an acmap object

Description

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

Usage

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

Other functions for working with map data: acmap(), agReactivityAdjustments(), as.json(), edit_agNames(), edit_srNames(), keepBestOptimization(), keepSingleOptimization(), layerNames(), orderPoints, read.acmap(), read.titerTable(), removePoints, save.acmap(), save.coords(), save.titerTable(), subsetCommonPoints, subsetMap()

Racmacs documentation built on June 22, 2024, 11:33 a.m.