Merging maps

Functions to merge together two tables or maps.

mergeMaps(
  ...,
  method = "table",
  number_of_dimensions,
  number_of_optimizations,
  minimum_column_basis = "none",
  optimizer_options = list(),
  merge_options = list(),
  verbose = TRUE
)

Arguments

...: acmaps to merge provided as either a list, or a series of separate arguments
method: The merge method to use, see details.
number_of_dimensions: For merging that generates new optimization runs, the number of dimensions.
number_of_optimizations: For merging that generates new optimization runs, the number of optimization runs to do.
minimum_column_basis: For merging that generates new optimization runs, the minimum column basis to use.
optimizer_options: For merging that generates new optimization runs, optimizer settings (see RacOptimizer.options()).
merge_options: Options to use when merging titers (see RacMerge.options()).
verbose: Should progress messages be output?

Value

Returns the merged map object

Details

Maps can be merged in a number of ways depending upon the desired result.

Method 'table'

As you would expect, this merges the tables of the two maps but does not attempt to create any new optimizations and any existing optimizations are lost.

Method 'reoptimized-merge'

This merges the tables and then does a specified number of fresh optimizations from random starting coordinates, ignoring any pre-existing optimization runs. It's exactly the same as doing a 'table' merge and running optimizeMap() on the merged table.

Method 'incremental-merge'

This takes the currently selected optimization in the first map and then merges in the additional maps in turn. Each time any points not already found in the first map (or the last map in the incremental merge chain) are randomised and everything is relaxed, this is repeated the specified number of times and the process is repeated.

Method 'frozen-overlay'

This fixes the positions of points in each map and tries to best match them simply through re-orientation. Once the best re-orientation is found, points that are in common between the maps are moved to the average position.

Method 'relaxed-overlay'

This is the same as the frozen-overlay but points in the resulting map are then allowed to relax.

Method 'frozen-merge'

In this version, positions of all points in the first map are fixed and remain fixed, so the original map does not change. The second map is then realigned to the first as closely as possible and then all the new points appearing in the second map are allowed to relax into their new positions. This is a way to merge in new antigens and sera into a map without affecting the first one at all (and was first implemented in lisp).