procrustesData {Racmacs}

Return procrustes data on a map comparison

Description

Returns information about how similar point positions are in two maps, to get an idea of how similar antigenic positions are in for example maps made from two different datasets.

Usage

procrustesData(
  map,
  comparison_map,
  optimization_number = 1,
  comparison_optimization_number = 1,
  antigens = TRUE,
  sera = TRUE,
  translation = TRUE,
  scaling = FALSE
)

Arguments

map

The acmap data object

comparison_map

The acmap data object to procrustes against

optimization_number

The map optimization to use in the procrustes calculation (other optimization runs are discarded)

comparison_optimization_number

The optimization run int the comparison map to compare against

antigens

Antigens to include (specified by name or index or TRUE/FALSE for all/none)

sera

Sera to include (specified by name or index or TRUE/FALSE for all/none)

translation

Should translation be allowed

scaling

Should scaling be allowed (generally not recommended unless comparing maps made with different assays)

Value

Returns a list with information on antigenic distances between the aligned maps, and the rmsd of the point differences split by antigen points, serum points and total, or all points. The distances are a vector matching the number of points in the main map, with NA in the position of any points not found in the comparison map.

See Also

Other functions to compare maps: matchStrains, procrustesMap(), realignMap(), realignOptimizations()