Antigenic Cartography Macros

Documentation for package ‘Racmacs’ version 1.2.9

Help Pages

-- 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