Working with map data

acmap()

Generate a new acmap object

addOptimization()

Add a new optimization to an acmap object

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

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

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

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

agTriangulationBlobSize() srTriangulationBlobSize()

Fetch information on triangulation blob size

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

Viewing maps

RacViewer()

Create a RacViewer widget

RacViewer.options()

Set viewer options

export_viewer()

Export the map viewer

grid.plot.acmap()

Plot an antigenic map using the grid system

plot(<acmap>)

Plot an antigenic map

setLegend()

Set acmap legend

snapshotMap()

Create a map snapshot

view()

S3 method for viewing objects

view(<acmap>)

Viewing racmap objects

view(<default>)

Default method for viewing objects

Map attributes

General attributes

numAntigens() numSera() numPoints() numOptimizations()

Get acmap attributes

dilutionStepsize() `dilutionStepsize<-`()

Get or set the dilution stepsize associated with a map

mapName() `mapName<-`()

Getting and setting the map name

titerTable() `titerTable<-`() titerTableFlat() `titerTableFlat<-`()

Getting and setting map titers

titerTableLayers() `titerTableLayers<-`()

Getting and setting titer table layers

Antigen and sera attributes

agNames() `agNames<-`() agIDs() `agIDs<-`() agDates() `agDates<-`() agNamesFull() agNamesAbbreviated() agReference() agPassage()

Getting and setting antigen attributes

agGroups() `agGroups<-`()

Getting and setting antigen groups

agSequences() `agSequences<-`()

Getting and setting antigen sequence information

agClades() srClades() `agClades<-`() `srClades<-`()

Getting and setting point clade information

srNames() `srNames<-`() srIDs() `srIDs<-`() srDates() `srDates<-`() srNamesFull() srNamesAbbreviated() srReference() srPassage()

Getting and setting sera attributes

srGroups() `srGroups<-`()

Getting and setting sera groups

srSequences() `srSequences<-`()

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<-`() agReactivityAdjustments() `agReactivityAdjustments<-`()

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

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

Using the shiny app

runGUI()

Open the Racmacs GUI

Utilities

standardizeStrainNames()

Standardize strain names