procrustesMap {Racmacs}

Return procrustes information

Description

Returns information from one map procrusted to another.

Usage

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

keep_optimizations

Should all optimization runs be kept or only the one to which the procrustes was applied.

Value

Returns an acmap object with procrustes information added, which will be shown when the map is plotted. To avoid ambiguity about which optimization run the procrustes was applied to, only the optimization run specified by optimization_number is kept in the map returned.

See Also

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