Getting and setting of antigen and serum coordinates in a map optimization run (by default the currently selected one).

agCoords(map, optimization_number = 1)

srCoords(map, optimization_number = 1)

ptCoords(map, optimization_number = 1)

ptCoords(map, optimization_number = 1) <- value

agCoords(map, optimization_number = 1) <- value

srCoords(map, optimization_number = 1) <- value

Arguments

map The acmap object The optimization number from which to get / set the coordinates A matrix of new coordinates to set

Details

These functions get and set point coordinates in a map. By default these coordinates refer to the currently selected optimization run, unless otherwise specified through the optimization_number argument.

99\ want to use but you should note that the outputs are actually the map base coordinates after the transformation and translation associated with the optimization run has been applied (see mapTransformation() and mapTranslation() for more details). When you set the antigen or serum coordinates through these functions, the transformed coordinates are "baked" in and the map transformation and translation are reset. Consequently if you want to apply a transformation to all coordinates generally, you are better off modifying the map translation and transformation directly, as is done by functions like rotateMap() and translateMap().

agBaseCoords() srBaseCoords() mapTransformation() mapTranslation()
Other map optimization attribute functions: colBases(), mapComment(), mapDimensions(), mapStress(), mapTransformation(), ptBaseCoords()