RacMerge.options        Set acmap merge options
RacOptimizer.options    Set acmap optimization options
RacViewer               Create a RacViewer widget
RacViewer-shiny         Shiny bindings for RacViewer
RacViewer.options       Set viewer options
acmap                   Generate a new acmap object
acmapAttributes         Get acmap attributes
addOptimization         Add a new optimization to an acmap object
adjustedLogTiterTable   Get the reactivity adjusted log titer table
adjustedTiterTable      Get the reactivity adjusted titer table
agAttributes            Getting and setting antigen attributes
agCohesion              Check map cohesion
agGroups                Getting and setting antigen groups
agHomologousSr          Get homologous sera for each antigen
agLabIDs                Getting and setting antigen lab id information
agReactivityAdjustments
                        Get and set antigen reactivity adjustments
agSequences             Getting and setting antigen sequence
                        information
applyMapTransform       Apply the current map transformation
applyPlotspec           Apply a plotspec from another acmap
as.json                 Convert map to json format
blob                    Plot a blob object
blobsize                Calculate size of a blob object
bootstrapBlobs          Calculate bootstrap blob data for an antigenic
                        map
bootstrapMap            Perform a bootstrap on a map
checkHemisphering       Check for hemisphering or trapped points
colBases                Getting and setting column bases
deprecated_functions    Deprecated functions
dilutionStepsize        Get or set the dilution stepsize associated
                        with a map
dimensionTestMap        Perform dimension testing on a map object
edit_agNames            Edit antigen names in an acmap
edit_srNames            Edit sera names in an acmap
export_viewer           Export the map viewer
getOptimization         Get optimization details from an acmap object
ggplot.acmap            Plot an antigenic map using ggplot
htmlAdjustedTiterTable
                        Return an html formatted titer table with
                        antigen reactivity adjustments applied
htmlMergeReport         Return an html formatted merge report
htmlTiterTable          Return an html formatted titer table
keepBestOptimization    Keep only the lowest stress map optimization
keepOptimizations       Keep specified optimization runs
keepSingleOptimization
                        Keep only a single optimization run
layerNames              Get and set map layer names
listOptimizations       Get all optimization details from an acmap
                        object
logtiterTable           Get the log titers from an acmap
logtiterTableLayers     Return a list of logtiter table layers
make.acmap              Make an antigenic map from scratch
map-table-distances     Plot map vs table distances
mapBootstrapCoords      Get bootstrap coordinates associated with a map
mapComment              Get or set an optimization run comment
mapDescription          Getting and setting the map description
mapDimensions           Get the current map dimensions
mapDistances            Return calculated map distances for an acmap
mapGadget               Open a shiny gadget to view the map
mapName                 Getting and setting the map name
mapRelaxed              Check if a map has been fully relaxed
mapResiduals            Get a table of residuals from an acmap
mapStress               Calculate the current map stress
mapTransformation       Reading map transformation data
matchStrains            Find matching antigens or sera between 2 maps
mergeMaps               Merging maps
mergeReport             Return a merge report
moveTrappedPoints       Move trapped points
optimizationProperties
                        Get optimization properties
optimizeAgReactivity    Optimize antigen reactivity adjustments
optimizeMap             Optimize an acmap
orderPoints             Order antigens and sera
plot.acmap              Plot an antigenic map
pointStress             Get individual point stress
procrustesData          Return procrustes data on a map comparison
procrustesMap           Return procrustes information
ptAnnotations           Getting and setting point annotation
                        information
ptBaseCoords            Getting and setting base coordinates
ptBootstrapBlob         Get antigen or serum bootstrap blob information
ptBootstrapCoords       Get antigen or serum bootstrap coordinates
                        information
ptClades                Getting and setting point clade information
ptCoords                Getting and setting point coordinates
ptDrawingOrder          Get and set point drawing order in map
ptLeverage              Calculate point leverage
ptOpacity               Set point opacity in a map
ptStyles                Getting and setting point plotting styles
ptTriangulationBlob     Get antigen or serum triangulation blob
                        information
randomizeCoords         Randomize map coordinates
read.acmap              Read in acmap data from a file
read.titerTable         Read in a table of titer data
realignMap              Realign map to match another
realignOptimizations    Realigns optimizations in the map
recalculateStress       Recalculate the stress associated with an acmap
                        optimization
reflectMap              Reflect a map
relaxMap                Relax a map
relaxMapOneStep         Relax a map one step in the optimiser
removeOptimizations     Remove map optimizations
removePoints            Remove antigens and sera
rotateMap               Rotate a map
runGUI                  Open the Racmacs GUI
save.acmap              Save acmap data to a file
save.coords             Save acmap coordinate data to a file
save.titerTable         Save titer data to a file
setLegend               Set acmap legend
sortOptimizations       Sort optimizations by stress
splitTiterLayers        Split a map made up from titer layers into a
                        list of separate maps each with a titer table
                        corresponding to one of the layers
srAttributes            Getting and setting sera attributes
srGroups                Getting and setting sera groups
srHomologousAgs         Get and set homologous antigens for sera
srSequences             Getting and setting sera sequence information
standardizeStrainNames
                        Standardize strain names
stressTable             Get a stress table from an acmap
subsetCommonPoints      Remove antigens and sera
subsetMap               Subset an antigenic map
tableColbases           Calculate column bases for a titer table
tableDistances          Return calculated table distances for an acmap
titerTable              Getting and setting map titers
titerTableFlat          Getting and setting the flat titer table
titerTableLayers        Getting and setting titer table layers
translateMap            Translate a map
triangulationBlobs      Calculate triangulation blobs data for an
                        antigenic map
unstableMaps            Notes on unstable maps
view                    S3 method for viewing objects
view.acmap              Viewing racmap objects
view.default            Default method for viewing objects
