# Antigenic Cartography Macros

## Documentation for package ‘Racmacs’ version 1.2.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H K L M N O P R S T U V

## -- A --

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
agAnnotations | Getting and setting point annotation information
agAnnotations<- | Getting and setting point annotation information
agAspect | Getting and setting point plotting styles
agAspect<- | Getting and setting point plotting styles
agAttributes | Getting and setting antigen attributes
agBaseCoords | Getting and setting base coordinates
agBaseCoords<- | Getting and setting base coordinates
agBootstrapBlob | Get antigen or serum bootstrap blob information
agBootstrapBlobs | Get antigen or serum bootstrap blob information
agBootstrapCoords | Get antigen or serum bootstrap coordinates information
agClades | Getting and setting point clade information
agClades<- | Getting and setting point clade information
agCohesion | Check map cohesion
agContinent | Getting and setting antigen attributes
agContinent<- | Getting and setting antigen attributes
agCoords | Getting and setting point coordinates
agCoords<- | Getting and setting point coordinates
agDates | Getting and setting antigen attributes
agDates<- | Getting and setting antigen attributes
agExtra | Getting and setting antigen attributes
agExtra<- | Getting and setting antigen attributes
agFill | Getting and setting point plotting styles
agFill<- | Getting and setting point plotting styles
agGroups | Getting and setting antigen groups
agGroups<- | Getting and setting antigen groups
agHomologousSr | Get homologous sera for each antigen
agIDs | Getting and setting antigen attributes
agIDs<- | Getting and setting antigen attributes
agLabIDs | Getting and setting antigen lab id information
agLabIDs<- | Getting and setting antigen lab id information
agLeverage | Calculate point leverage
agLineage | Getting and setting antigen attributes
agLineage<- | Getting and setting antigen attributes
agNames | Getting and setting antigen attributes
agNames<- | Getting and setting antigen attributes
agNucleotideSequences | Getting and setting antigen sequence information
agNucleotideSequences<- | Getting and setting antigen sequence information
agOpacity<- | Set point opacity in a map
agOutline | Getting and setting point plotting styles
agOutline<- | Getting and setting point plotting styles
agOutlineWidth | Getting and setting point plotting styles
agOutlineWidth<- | Getting and setting point plotting styles
agPassage | Getting and setting antigen attributes
agPassage<- | Getting and setting antigen attributes
agReactivityAdjustments | Get and set antigen reactivity adjustments
agReactivityAdjustments<- | Get and set antigen reactivity adjustments
agReassortant | Getting and setting antigen attributes
agReassortant<- | Getting and setting antigen attributes
agReference | Getting and setting antigen attributes
agReference<- | Getting and setting antigen attributes
agRotation | Getting and setting point plotting styles
agRotation<- | Getting and setting point plotting styles
agSequences | Getting and setting antigen sequence information
agSequences<- | Getting and setting antigen sequence information
agShape | Getting and setting point plotting styles
agShape<- | Getting and setting point plotting styles
agShown | Getting and setting point plotting styles
agShown<- | Getting and setting point plotting styles
agSize | Getting and setting point plotting styles
agSize<- | Getting and setting point plotting styles
agStress | Get individual point stress
agStressPerTiter | Get individual point stress
agStrings | Getting and setting antigen attributes
agStrings<- | Getting and setting antigen attributes
agTriangulationBlob | Get antigen or serum triangulation blob information
agTriangulationBlobs | Get antigen or serum triangulation blob information
allMapDimensions | Get optimization properties
allMapStresses | Get optimization properties
applyMapTransform | Apply the current map transformation
applyPlotspec | Apply a plotspec from another acmap
as.json | Convert map to json format

## -- B --

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

## -- C --

checkHemisphering | Check for hemisphering or trapped points
colBases | Getting and setting column bases

## -- D --

deprecated_functions | Deprecated functions
dilutionStepsize | Get or set the dilution stepsize associated with a map
dilutionStepsize<- | Get or set the dilution stepsize associated with a map
dimensionTestMap | Perform dimension testing on a map object

## -- E --

edit_agNames | Edit antigen names in an acmap
edit_srNames | Edit sera names in an acmap
export_viewer | Export the map viewer

## -- F --

fixedColBases | Getting and setting column bases
fixedColBases<- | Getting and setting column bases

## -- G --

getOptimization | Get optimization details from an acmap object
ggplot.acmap | Plot an antigenic map using ggplot

## -- H --

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

## -- K --

keepBestOptimization | Keep only the lowest stress map optimization
keepOptimizations | Keep specified optimization runs
keepSingleOptimization | Keep only a single optimization run

## -- L --

layerNames | Get and set map layer names
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

## -- M --

make.acmap | Make an antigenic map from scratch
map-table-distances | Plot map vs table distances
mapBootstrapCoords | Get bootstrap coordinates associated with a map
mapBootstrap_agCoords | Get bootstrap coordinates associated with a map
mapBootstrap_ptBaseCoords | Get bootstrap coordinates associated with a map
mapBootstrap_srCoords | Get bootstrap coordinates associated with a map
mapCohesion | Check map cohesion
mapComment | Get or set an optimization run comment
mapComment<- | Get or set an optimization run comment
mapDescription | Getting and setting the map description
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
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
mapTransformation<- | Reading map transformation data
mapTranslation | Reading map transformation data
mapTranslation<- | Reading map transformation data
matchStrains | Find matching antigens or sera between 2 maps
match_mapAntigens | Find matching antigens or sera between 2 maps
match_mapSera | Find matching antigens or sera between 2 maps
mergeMaps | Merging maps
mergeReport | Return a merge report
minColBasis | Getting and setting column bases
minColBasis<- | Getting and setting column bases
moveTrappedPoints | Move trapped points

## -- N --

numAntigens | Get acmap attributes
numLayers | Get acmap attributes
numOptimizations | Get acmap attributes
numPoints | Get acmap attributes
numSera | Get acmap attributes
numSeraGroups | Get acmap attributes

## -- O --

optimizationProperties | Get optimization properties
optimizeAgReactivity | Optimize antigen reactivity adjustments
optimizeMap | Optimize an acmap
orderAntigens | Order antigens and sera
orderPoints | Order antigens and sera
orderSera | Order antigens and sera

## -- P --

plot.acmap | Plot an antigenic map
plotly_map_table_distance | Plot map vs table distances
plot_map_table_distance | Plot map vs table distances
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
ptBootstrapBlobs | 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
ptCoords<- | Getting and setting point coordinates
ptDrawingOrder | Get and set point drawing order in map
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
ptTriangulationBlobs | Get antigen or serum triangulation blob information

## -- R --

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
RacViewerOutput | Shiny bindings for RacViewer
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
removeAntigens | Remove antigens and sera
removeOptimizations | Remove map optimizations
removePoints | Remove antigens and sera
removeSera | Remove antigens and sera
renderRacViewer | Shiny bindings for RacViewer
rotateMap | Rotate a map
runGUI | Open the Racmacs GUI

## -- S --

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
srAnnotations | Getting and setting point annotation information
srAnnotations<- | Getting and setting point annotation information
srAspect | Getting and setting point plotting styles
srAspect<- | Getting and setting point plotting styles
srAttributes | Getting and setting sera attributes
srBaseCoords | Getting and setting base coordinates
srBaseCoords<- | Getting and setting base coordinates
srBootstrapBlob | Get antigen or serum bootstrap blob information
srBootstrapBlobs | Get antigen or serum bootstrap blob information
srBootstrapCoords | Get antigen or serum bootstrap coordinates information
srClades | Getting and setting point clade information
srClades<- | Getting and setting point clade information
srCohesion | Check map cohesion
srCoords | Getting and setting point coordinates
srCoords<- | Getting and setting point coordinates
srDates | Getting and setting sera attributes
srDates<- | Getting and setting sera attributes
srExtra | Getting and setting sera attributes
srExtra<- | Getting and setting sera attributes
srFill | Getting and setting point plotting styles
srFill<- | Getting and setting point plotting styles
srGroups | Getting and setting sera groups
srGroups<- | Getting and setting sera groups
srHomologousAgs | Get and set homologous antigens for sera
srHomologousAgs<- | Get and set homologous antigens for sera
srIDs | Getting and setting sera attributes
srIDs<- | Getting and setting sera attributes
srLeverage | Calculate point leverage
srLineage | Getting and setting sera attributes
srLineage<- | Getting and setting sera attributes
srNames | Getting and setting sera attributes
srNames<- | Getting and setting sera attributes
srNucleotideSequences | Getting and setting sera sequence information
srNucleotideSequences<- | Getting and setting sera sequence information
srOpacity<- | Set point opacity in a map
srOutline | Getting and setting point plotting styles
srOutline<- | Getting and setting point plotting styles
srOutlineWidth | Getting and setting point plotting styles
srOutlineWidth<- | Getting and setting point plotting styles
srPassage | Getting and setting sera attributes
srPassage<- | Getting and setting sera attributes
srReassortant | Getting and setting sera attributes
srReassortant<- | Getting and setting sera attributes
srReference | Getting and setting sera attributes
srReference<- | Getting and setting sera attributes
srRotation | Getting and setting point plotting styles
srRotation<- | Getting and setting point plotting styles
srSequences | Getting and setting sera sequence information
srSequences<- | Getting and setting sera sequence information
srShape | Getting and setting point plotting styles
srShape<- | Getting and setting point plotting styles
srShown | Getting and setting point plotting styles
srShown<- | Getting and setting point plotting styles
srSize | Getting and setting point plotting styles
srSize<- | Getting and setting point plotting styles
srSpecies | Getting and setting sera attributes
srSpecies<- | Getting and setting sera attributes
srStress | Get individual point stress
srStressPerTiter | Get individual point stress
srStrings | Getting and setting sera attributes
srStrings<- | Getting and setting sera attributes
srTriangulationBlob | Get antigen or serum triangulation blob information
srTriangulationBlobs | Get antigen or serum triangulation blob information
standardizeStrainNames | Standardize strain names
stressBlobs | Deprecated functions
stressTable | Get a stress table from an acmap
subsetCommonAgs | Remove antigens and sera
subsetCommonPoints | Remove antigens and sera
subsetCommonSrGroups | Remove antigens and sera
subsetMap | Subset an antigenic map

## -- T --

tableColbases | Calculate column bases for a titer table
tableDistances | Return calculated table distances for an acmap
titerLeverage | Calculate point leverage
titerTable | Getting and setting map titers
titerTable<- | Getting and setting map titers
titerTableFlat | Getting and setting the flat titer table
titerTableFlat<- | Getting and setting the flat titer table
titerTableLayers | Getting and setting titer table layers
titerTableLayers<- | Getting and setting titer table layers
translateMap | Translate a map
triangulationBlobs | Calculate triangulation blobs data for an antigenic map

## -- U --

unstableMaps | Notes on unstable maps

## -- V --

view | S3 method for viewing objects
view.acmap | Viewing racmap objects
view.default | Default method for viewing objects