Function reference • Racmacs

Working with map data
`acmap()`	Generate a new acmap object
`addOptimization()`	Add a new optimization to an acmap object
`agReactivityAdjustments()` `agReactivityAdjustments<-`()	Get and set antigen reactivity adjustments
`as.json()`	Convert map to json format
`edit_agNames()`	Edit antigen names in an acmap
`edit_srNames()`	Edit sera names in an acmap
`keepBestOptimization()`	Keep only the lowest stress map optimization
`keepSingleOptimization()`	Keep only a single optimization run
`layerNames()` `layerNames<-`()	Get and set map layer names
`orderAntigens()` `orderSera()`	Order antigens and sera
`read.acmap()`	Read in acmap data from a file
`read.titerTable()`	Read in a table of titer data
`removeAntigens()` `removeSera()`	Remove antigens and sera
`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
`subsetCommonAgs()` `subsetCommonSrGroups()`	Remove antigens and sera
`subsetMap()`	Subset an antigenic map
Optimizing maps
`RacOptimizer.options()`	Set acmap optimization options
`make.acmap()`	Make an antigenic map from scratch
`moveTrappedPoints()`	Move trapped points
`optimizeMap()`	Optimize an acmap
`randomizeCoords()`	Randomize map coordinates
`relaxMap()`	Relax a map
`relaxMapOneStep()`	Relax a map one step in the optimiser
`keepOptimizations()`	Keep specified optimization runs
`allMapStresses()` `allMapDimensions()`	Get optimization properties
`removeOptimizations()`	Remove map optimizations
`sortOptimizations()`	Sort optimizations by stress
Testing maps
`bootstrapBlobs()`	Calculate bootstrap blob data for an antigenic map
`bootstrapMap()`	Perform a bootstrap on a map
`checkHemisphering()`	Check for hemisphering or trapped points
`dimensionTestMap()`	Perform dimension testing on a map object
`logtiterTable()`	Get the log titers from an acmap
`plot_map_table_distance()` `plotly_map_table_distance()`	Plot map vs table distances
`mapBootstrap_ptBaseCoords()` `mapBootstrap_agCoords()` `mapBootstrap_srCoords()`	Get bootstrap coordinates associated with a map
`agCohesion()` `srCohesion()` `mapCohesion()`	Check map cohesion
`mapDistances()`	Return calculated map distances for an acmap
`mapRelaxed()`	Check if a map has been fully relaxed
`mapResiduals()`	Get a table of residuals from an acmap
`agStress()` `srStress()` `srStressPerTiter()` `agStressPerTiter()`	Get individual point stress
`agBootstrapBlob()` `srBootstrapBlob()` `agBootstrapBlobs()` `srBootstrapBlobs()` `ptBootstrapBlobs()`	Get antigen or serum bootstrap blob information
`ptBootstrapCoords()` `agBootstrapCoords()` `srBootstrapCoords()`	Get antigen or serum bootstrap coordinates information
`agLeverage()` `srLeverage()` `titerLeverage()`	Calculate point leverage
`agTriangulationBlob()` `srTriangulationBlob()` `agTriangulationBlobs()` `srTriangulationBlobs()` `ptTriangulationBlobs()`	Get antigen or serum triangulation blob information
`recalculateStress()`	Recalculate the stress associated with an acmap optimization
`stressTable()`	Get a stress table from an acmap
`tableColbases()`	Calculate column bases for a titer table
`tableDistances()`	Return calculated table distances for an acmap
`triangulationBlobs()`	Calculate triangulation blobs data for an antigenic map
`unstableMaps`	Notes on unstable maps
Viewing maps
`RacViewer()`	Create a RacViewer widget
`RacViewer.options()`	Set viewer options
`export_viewer()`	Export the map viewer
`ggplot(<acmap>)`	Plot an antigenic map using ggplot
`mapGadget()`	Open a shiny gadget to view the map
`plot(<acmap>)`	Plot an antigenic map
`setLegend()`	Set acmap legend
`view()`	S3 method for viewing objects
`view(<acmap>)`	Viewing racmap objects
`view(<default>)`	Default method for viewing objects
Map attributes
General attributes
`numAntigens()` `numSera()` `numSeraGroups()` `numPoints()` `numOptimizations()` `numLayers()`	Get acmap attributes
`adjustedLogTiterTable()`	Get the reactivity adjusted log titer table
`adjustedTiterTable()`	Get the reactivity adjusted titer table
`dilutionStepsize()` `dilutionStepsize<-`()	Get or set the dilution stepsize associated with a map
`logtiterTableLayers()`	Return a list of logtiter table layers
`mapDescription()` `mapDescription<-`()	Getting and setting the map description
`mapName()` `mapName<-`()	Getting and setting the map name
`titerTable()` `titerTable<-`()	Getting and setting map titers
`titerTableFlat()` `titerTableFlat<-`()	Getting and setting the flat titer table
`titerTableLayers()` `titerTableLayers<-`()	Getting and setting titer table layers
Antigen and sera attributes
`agIDs()` `agIDs<-`() `agDates()` `agDates<-`() `agReference()` `agReference<-`() `agNames()` `agNames<-`() `agExtra()` `agExtra<-`() `agPassage()` `agPassage<-`() `agLineage()` `agLineage<-`() `agReassortant()` `agReassortant<-`() `agStrings()` `agStrings<-`() `agContinent()` `agContinent<-`()	Getting and setting antigen attributes
`agGroups()` `agGroups<-`()	Getting and setting antigen groups
`agHomologousSr()`	Get homologous sera for each antigen
`agLabIDs()` `agLabIDs<-`()	Getting and setting antigen lab id information
`agSequences()` `agSequences<-`() `agNucleotideSequences()` `agNucleotideSequences<-`()	Getting and setting antigen sequence information
`agAnnotations()` `srAnnotations()` `agAnnotations<-`() `srAnnotations<-`()	Getting and setting point annotation information
`agClades()` `srClades()` `agClades<-`() `srClades<-`()	Getting and setting point clade information
`srIDs()` `srIDs<-`() `srDates()` `srDates<-`() `srReference()` `srReference<-`() `srNames()` `srNames<-`() `srExtra()` `srExtra<-`() `srPassage()` `srPassage<-`() `srLineage()` `srLineage<-`() `srReassortant()` `srReassortant<-`() `srStrings()` `srStrings<-`() `srSpecies()` `srSpecies<-`()	Getting and setting sera attributes
`srGroups()` `srGroups<-`()	Getting and setting sera groups
`srHomologousAgs()` `srHomologousAgs<-`()	Get and set homologous antigens for sera
`srSequences()` `srSequences<-`() `srNucleotideSequences()` `srNucleotideSequences<-`()	Getting and setting sera sequence information
Optimization run attributes
`listOptimizations()`	Get all optimization details from an acmap object
`getOptimization()`	Get optimization details from an acmap object
`minColBasis()` `minColBasis<-`() `fixedColBases()` `fixedColBases<-`()	Getting and setting column bases
`mapComment()` `mapComment<-`()	Get or set an optimization run comment
`mapDimensions()`	Get the current map dimensions
`mapStress()`	Calculate the current map stress
`mapTransformation()` `mapTransformation<-`() `mapTranslation()` `mapTranslation<-`()	Reading map transformation data
`ptBaseCoords()` `agBaseCoords()` `agBaseCoords<-`() `srBaseCoords()` `srBaseCoords<-`()	Getting and setting base coordinates
`agCoords()` `srCoords()` `ptCoords()` `ptCoords<-`() `agCoords<-`() `srCoords<-`()	Getting and setting point coordinates
Point plotting styles
`applyPlotspec()`	Apply a plotspec from another acmap
`ptDrawingOrder()` `ptDrawingOrder<-`()	Get and set point drawing order in map
`agOpacity<-`() `srOpacity<-`()	Set point opacity in a map
`agShown()` `srShown()` `agShown<-`() `srShown<-`() `agSize()` `srSize()` `agSize<-`() `srSize<-`() `agFill()` `srFill()` `agFill<-`() `srFill<-`() `agOutline()` `srOutline()` `agOutline<-`() `srOutline<-`() `agOutlineWidth()` `srOutlineWidth()` `agOutlineWidth<-`() `srOutlineWidth<-`() `agRotation()` `srRotation()` `agRotation<-`() `srRotation<-`() `agAspect()` `srAspect()` `agAspect<-`() `srAspect<-`() `agShape()` `srShape()` `agShape<-`() `srShape<-`()	Getting and setting point plotting styles
Map transformations
`applyMapTransform()`	Apply the current map transformation
`reflectMap()`	Reflect a map
`rotateMap()`	Rotate a map
`translateMap()`	Translate a map
Comparing maps
`match_mapAntigens()` `match_mapSera()`	Find matching antigens or sera between 2 maps
`procrustesData()`	Return procrustes data on a map comparison
`procrustesMap()`	Return procrustes information
`realignMap()`	Realign map to match another
`realignOptimizations()`	Realigns optimizations in the map
Merging maps
`RacMerge.options()`	Set acmap merge options
`htmlMergeReport()`	Return an html formatted merge report
`mergeMaps()`	Merging maps
`mergeReport()`	Return a merge report
`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
Additional plotting functions
`blob()`	Plot a blob object
`blobsize()`	Calculate size of a blob object
Using the shiny app
`RacViewerOutput()` `renderRacViewer()`	Shiny bindings for RacViewer
`runGUI()`	Open the Racmacs GUI
`view(<acmap>)`	Viewing racmap objects
Viewing titers
`htmlTiterTable()`	Return an html formatted titer table
`htmlAdjustedTiterTable()`	Return an html formatted titer table with antigen reactivity adjustments applied
Utilities
`standardizeStrainNames()`	Standardize strain names
Experimental functions
`optimizeAgReactivity()`	Optimize antigen reactivity adjustments
Deprecated functions
`stressBlobs()`	Deprecated functions

Reference

Working with map data

Optimizing maps

Testing maps

Viewing maps

Map attributes

General attributes

Antigen and sera attributes

Optimization run attributes

Point plotting styles

Map transformations

Comparing maps

Merging maps

Additional plotting functions

Using the shiny app

Viewing titers

Utilities

Experimental functions

Deprecated functions