Take an acmap object with a table of titer data and perform optimization runs to try and find the best arrangement of antigens and sera to represent their antigenic similarity. Optimizations generated from each run with different random starting conditions will be added to the acmap object.
optimizeMap( map, number_of_dimensions, number_of_optimizations, minimum_column_basis = "none", fixed_column_bases = NULL, ag_reactivity_adjustments = NULL, titer_weights = NULL, sort_optimizations = TRUE, verbose = TRUE, options = list() )
map  The acmap data object 

number_of_dimensions  The number of dimensions for the new map 
number_of_optimizations  The number of optimization runs to perform 
minimum_column_basis  The minimum column basis to use (see details) 
fixed_column_bases  A vector of fixed values to use as column bases directly, rather than calculating them from the titer table. 
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. 
titer_weights  An optional matrix of weights to assign each titer when optimizing 
sort_optimizations  Should optimizations be sorted by stress afterwards? 
verbose  Should progress messages be reported, see also

options  List of named optimizer options, see 
Returns the acmap object updated with new optimizations.
This is the core function to run map optimizations. In essence, for
each optimization run, points are randomly distributed in ndimensional
space, the LBFGS gradientbased optimization algorithm is applied to move
points into an optimal position. Depending on the map, this may not be a
trivial optimization process and results will depend upon the starting
conditions so multiple optimization runs may be required. For a full
explanation see vignette("introtoantigeniccartography")
.
vector of fixed column bases for each sera, where NA is specified (the
default) column bases will be calculated according to the
minimum_column_basis
setting. Again for a full explanation of column
bases and what they mean see vignette("introtoantigeniccartography")
.
See relaxMap()
for optimizing a given optimization starting from
its current coordinates.
Other map optimization functions:
RacOptimizer.options()
,
make.acmap()
,
moveTrappedPoints()
,
randomizeCoords()
,
relaxMapOneStep()
,
relaxMap()