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