Package: Racmacs 1.2.9

Sam Wilks

Racmacs: Antigenic Cartography Macros

A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.

Authors:Sam Wilks [aut, cre]

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Racmacs.pdf |Racmacs.html✨
Racmacs/json (API)
NEWS

# Install 'Racmacs' in R:
install.packages('Racmacs', repos = c('https://acorg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/acorg/racmacs/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

8.52 score 20 stars 366 scripts 183 downloads 251 exports 81 dependencies

Last updated 4 months agofrom:f75f9cd2d6. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 13 2024
R-4.5-win-x86_64OKOct 13 2024
R-4.5-linux-x86_64OKOct 13 2024
R-4.4-win-x86_64OKOct 13 2024
R-4.4-mac-x86_64OKOct 13 2024
R-4.4-mac-aarch64OKOct 13 2024
R-4.3-win-x86_64OKOct 13 2024
R-4.3-mac-x86_64OKOct 13 2024
R-4.3-mac-aarch64OKOct 13 2024

Exports:acmapaddOptimizationadjustedLogTiterTableadjustedTiterTableagAnnotationsagAnnotations<-agAspectagAspect<-agBaseCoordsagBaseCoords<-agBootstrapBlobagBootstrapBlobsagBootstrapCoordsagCladesagClades<-agCohesionagContinentagContinent<-agCoordsagCoords<-agDatesagDates<-agExtraagExtra<-agFillagFill<-agGroupsagGroups<-agHomologousSragIDsagIDs<-agLabIDsagLabIDs<-agLeverageagLineageagLineage<-agNamesagNames<-agNucleotideSequencesagNucleotideSequences<-agOpacity<-agOutlineagOutline<-agOutlineWidthagOutlineWidth<-agPassageagPassage<-agReactivityAdjustmentsagReactivityAdjustments<-agReassortantagReassortant<-agReferenceagReference<-agRotationagRotation<-agSequencesagSequences<-agShapeagShape<-agShownagShown<-agSizeagSize<-agStressagStressPerTiteragStringsagStrings<-agTriangulationBlobagTriangulationBlobsallMapDimensionsallMapStressesapplyMapTransformapplyPlotspecas.jsonblobblobsizebootstrapBlobsbootstrapMapcheckHemispheringcolBasesdilutionStepsizedilutionStepsize<-dimensionTestMapedit_agNamesedit_srNamesexport_viewerfixedColBasesfixedColBases<-getOptimizationhtmlAdjustedTiterTablehtmlMergeReporthtmlTiterTablekeepBestOptimizationkeepOptimizationskeepSingleOptimizationlayerNameslayerNames<-listOptimizationslogtiterTablelogtiterTableLayersmake.acmapmapBootstrap_agCoordsmapBootstrap_srCoordsmapCohesionmapCommentmapComment<-mapDescriptionmapDescription<-mapDimensionsmapDistancesmapGadgetmapNamemapName<-mapRelaxedmapResidualsmapStressmapTransformationmapTransformation<-mapTranslationmapTranslation<-match_mapAntigensmatch_mapSeramergeMapsmergeReportminColBasisminColBasis<-moveTrappedPointsnumAntigensnumLayersnumOptimizationsnumPointsnumSeranumSeraGroupsoptimizeAgReactivityoptimizeMaporderAntigensorderSeraplot_map_table_distanceplotly_map_table_distanceprocrustesDataprocrustesMapptBaseCoordsptBootstrapBlobsptBootstrapCoordsptCoordsptCoords<-ptDrawingOrderptDrawingOrder<-ptTriangulationBlobsRacMerge.optionsRacOptimizer.optionsRacViewerRacViewer.optionsRacViewerOutputrandomizeCoordsread.acmapread.titerTablerealignMaprealignOptimizationsrecalculateStressreflectMaprelaxMaprelaxMapOneStepremoveAntigensremoveOptimizationsremoveSerarenderRacViewerrotateMaprunGUIsave.acmapsave.coordssave.titerTablesetLegendsortOptimizationssplitTiterLayerssrAnnotationssrAnnotations<-srAspectsrAspect<-srBaseCoordssrBaseCoords<-srBootstrapBlobsrBootstrapBlobssrBootstrapCoordssrCladessrClades<-srCohesionsrCoordssrCoords<-srDatessrDates<-srExtrasrExtra<-srFillsrFill<-srGroupssrGroups<-srHomologousAgssrHomologousAgs<-srIDssrIDs<-srLeveragesrLineagesrLineage<-srNamessrNames<-srNucleotideSequencessrNucleotideSequences<-srOpacity<-srOutlinesrOutline<-srOutlineWidthsrOutlineWidth<-srPassagesrPassage<-srReassortantsrReassortant<-srReferencesrReference<-srRotationsrRotation<-srSequencessrSequences<-srShapesrShape<-srShownsrShown<-srSizesrSize<-srSpeciessrSpecies<-srStresssrStressPerTitersrStringssrStrings<-srTriangulationBlobsrTriangulationBlobsstandardizeStrainNamesstressBlobsstressTablesubsetMaptableColbasestableDistancestiterLeveragetiterTabletiterTable<-titerTableLayerstranslateMaptriangulationBlobsupdate_ferret_seraNamesview

Dependencies:base64encbrotlibslibcachemclicolorspacecommonmarkcpp11crayondigestdplyrevaluatefansifarverfastmapFNNfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonlitekernlabKernSmoothknitrkslabelinglaterlatticelifecyclemagrittrMASSMatrixmclustmemoisemgcvmimemulticoolmunsellmvtnormnlmepillarpkgconfigpracmapromisesR6rapidjsonrrappdirsRColorBrewerRcppRcppArmadilloRcppEnsmallenRcppProgressrlangrmarchingcubesrmarkdownsassscalesshapeshinyshinyFilesshinyjssourcetoolstibbletidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml

Assessing map uncertainty

Rendered fromassessing_map_uncertainty.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-11-23
Started: 2022-03-01

Comparing maps

Rendered fromcomparing-maps.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-12-07
Started: 2020-03-05

Customising map appearance

Rendered fromcustomising-map-appearance.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-09-27
Started: 2023-09-27

Making an antigenic map from titer data

Rendered frommaking-a-map-from-scratch.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-12-07
Started: 2020-05-19

Merging maps

Rendered frommerging-maps.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2021-03-26
Started: 2020-03-05

Working with sequence data

Rendered fromadding-sequences.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-12-07
Started: 2020-07-24

Readme and manuals

Help Manual

Help pageTopics
Generate a new acmap objectacmap
Get acmap attributesacmapAttributes numAntigens numLayers numOptimizations numPoints numSera numSeraGroups
Add a new optimization to an acmap objectaddOptimization
Get the reactivity adjusted log titer tableadjustedLogTiterTable
Get the reactivity adjusted titer tableadjustedTiterTable
Getting and setting antigen attributesagAttributes agContinent agContinent<- agDates agDates<- agExtra agExtra<- agIDs agIDs<- agLineage agLineage<- agNames agNames<- agPassage agPassage<- agReassortant agReassortant<- agReference agReference<- agStrings agStrings<-
Check map cohesionagCohesion mapCohesion srCohesion
Getting and setting antigen groupsagGroups agGroups<-
Get homologous sera for each antigenagHomologousSr
Getting and setting antigen lab id informationagLabIDs agLabIDs<-
Get and set antigen reactivity adjustmentsagReactivityAdjustments agReactivityAdjustments<-
Getting and setting antigen sequence informationagNucleotideSequences agNucleotideSequences<- agSequences agSequences<-
Apply the current map transformationapplyMapTransform
Apply a plotspec from another acmapapplyPlotspec
Convert map to json formatas.json
Plot a blob objectblob
Calculate size of a blob objectblobsize
Calculate bootstrap blob data for an antigenic mapbootstrapBlobs
Perform a bootstrap on a mapbootstrapMap
Check for hemisphering or trapped pointscheckHemisphering
Getting and setting column basescolBases fixedColBases fixedColBases<- minColBasis minColBasis<-
Deprecated functionsdeprecated_functions stressBlobs
Get or set the dilution stepsize associated with a mapdilutionStepsize dilutionStepsize<-
Perform dimension testing on a map objectdimensionTestMap
Edit antigen names in an acmapedit_agNames
Edit sera names in an acmapedit_srNames
Export the map viewerexport_viewer
Get optimization details from an acmap objectgetOptimization
Plot an antigenic map using ggplotggplot.acmap
Return an html formatted titer table with antigen reactivity adjustments appliedhtmlAdjustedTiterTable
Return an html formatted merge reporthtmlMergeReport
Return an html formatted titer tablehtmlTiterTable
Keep only the lowest stress map optimizationkeepBestOptimization
Keep specified optimization runskeepOptimizations
Keep only a single optimization runkeepSingleOptimization
Get and set map layer nameslayerNames layerNames<-
Get all optimization details from an acmap objectlistOptimizations
Get the log titers from an acmaplogtiterTable
Return a list of logtiter table layerslogtiterTableLayers
Make an antigenic map from scratchmake.acmap
Plot map vs table distancesmap-table-distances plotly_map_table_distance plot_map_table_distance
Get bootstrap coordinates associated with a mapmapBootstrapCoords mapBootstrap_agCoords mapBootstrap_ptBaseCoords mapBootstrap_srCoords
Get or set an optimization run commentmapComment mapComment<-
Getting and setting the map descriptionmapDescription mapDescription<-
Get the current map dimensionsmapDimensions
Return calculated map distances for an acmapmapDistances
Open a shiny gadget to view the mapmapGadget
Getting and setting the map namemapName mapName<-
Check if a map has been fully relaxedmapRelaxed
Get a table of residuals from an acmapmapResiduals
Calculate the current map stressmapStress
Reading map transformation datamapTransformation mapTransformation<- mapTranslation mapTranslation<-
Find matching antigens or sera between 2 mapsmatchStrains match_mapAntigens match_mapSera
Merging mapsmergeMaps
Return a merge reportmergeReport
Move trapped pointsmoveTrappedPoints
Get optimization propertiesallMapDimensions allMapStresses optimizationProperties
Optimize antigen reactivity adjustmentsoptimizeAgReactivity
Optimize an acmapoptimizeMap
Order antigens and seraorderAntigens orderPoints orderSera
Plot an antigenic mapplot.acmap
Get individual point stressagStress agStressPerTiter pointStress srStress srStressPerTiter
Return procrustes data on a map comparisonprocrustesData
Return procrustes informationprocrustesMap
Getting and setting point annotation informationagAnnotations agAnnotations<- ptAnnotations srAnnotations srAnnotations<-
Getting and setting base coordinatesagBaseCoords agBaseCoords<- ptBaseCoords srBaseCoords srBaseCoords<-
Get antigen or serum bootstrap blob informationagBootstrapBlob agBootstrapBlobs ptBootstrapBlob ptBootstrapBlobs srBootstrapBlob srBootstrapBlobs
Get antigen or serum bootstrap coordinates informationagBootstrapCoords ptBootstrapCoords srBootstrapCoords
Getting and setting point clade informationagClades agClades<- ptClades srClades srClades<-
Getting and setting point coordinatesagCoords agCoords<- ptCoords ptCoords<- srCoords srCoords<-
Get and set point drawing order in mapptDrawingOrder ptDrawingOrder<-
Calculate point leverageagLeverage ptLeverage srLeverage titerLeverage
Set point opacity in a mapagOpacity<- ptOpacity srOpacity<-
Getting and setting point plotting stylesagAspect agAspect<- agFill agFill<- agOutline agOutline<- agOutlineWidth agOutlineWidth<- agRotation agRotation<- agShape agShape<- agShown agShown<- agSize agSize<- ptStyles srAspect srAspect<- srFill srFill<- srOutline srOutline<- srOutlineWidth srOutlineWidth<- srRotation srRotation<- srShape srShape<- srShown srShown<- srSize srSize<-
Get antigen or serum triangulation blob informationagTriangulationBlob agTriangulationBlobs ptTriangulationBlob ptTriangulationBlobs srTriangulationBlob srTriangulationBlobs
Set acmap merge optionsRacMerge.options
Set acmap optimization optionsRacOptimizer.options
Create a RacViewer widgetRacViewer
Shiny bindings for RacViewerRacViewer-shiny RacViewerOutput renderRacViewer
Set viewer optionsRacViewer.options
Randomize map coordinatesrandomizeCoords
Read in acmap data from a fileread.acmap
Read in a table of titer dataread.titerTable
Realign map to match anotherrealignMap
Realigns optimizations in the maprealignOptimizations
Recalculate the stress associated with an acmap optimizationrecalculateStress
Reflect a mapreflectMap
Relax a maprelaxMap
Relax a map one step in the optimiserrelaxMapOneStep
Remove map optimizationsremoveOptimizations
Remove antigens and seraremoveAntigens removePoints removeSera
Rotate a maprotateMap
Open the Racmacs GUIrunGUI
Save acmap data to a filesave.acmap
Save acmap coordinate data to a filesave.coords
Save titer data to a filesave.titerTable
Set acmap legendsetLegend
Sort optimizations by stresssortOptimizations
Split a map made up from titer layers into a list of separate maps each with a titer table corresponding to one of the layerssplitTiterLayers
Getting and setting sera attributessrAttributes srDates srDates<- srExtra srExtra<- srIDs srIDs<- srLineage srLineage<- srNames srNames<- srPassage srPassage<- srReassortant srReassortant<- srReference srReference<- srSpecies srSpecies<- srStrings srStrings<-
Getting and setting sera groupssrGroups srGroups<-
Get and set homologous antigens for serasrHomologousAgs srHomologousAgs<-
Getting and setting sera sequence informationsrNucleotideSequences srNucleotideSequences<- srSequences srSequences<-
Standardize strain namesstandardizeStrainNames
Get a stress table from an acmapstressTable
Remove antigens and serasubsetCommonAgs subsetCommonPoints subsetCommonSrGroups
Subset an antigenic mapsubsetMap
Calculate column bases for a titer tabletableColbases
Return calculated table distances for an acmaptableDistances
Getting and setting map titerstiterTable titerTable<-
Getting and setting the flat titer tabletiterTableFlat titerTableFlat<-
Getting and setting titer table layerstiterTableLayers titerTableLayers<-
Translate a maptranslateMap
Calculate triangulation blobs data for an antigenic maptriangulationBlobs
Notes on unstable mapsunstableMaps
S3 method for viewing objectsview
Viewing racmap objectsview.acmap
Default method for viewing objectsview.default