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]

Racmacs_1.2.9.tar.gz
Racmacs_1.2.9.tar.gz(r-4.5-noble)Racmacs_1.2.9.tar.gz(r-4.4-noble)
Racmacs_1.2.9.tgz(r-4.4-emscripten)Racmacs_1.2.9.tgz(r-4.3-emscripten)
Racmacs.pdf |Racmacs.html✨
Racmacs/json (API)
NEWS

# Install 'Racmacs' in R:

install.packages('Racmacs', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

5.34 score 366 scripts 193 downloads 251 exports 82 dependencies

Last updated 11 months agofrom:4c1a9a0f08. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-linux-x86_64	OK	Oct 26 2024

Exports:acmap addOptimization adjustedLogTiterTable adjustedTiterTable agAnnotations agAnnotations<-agAspect agAspect<-agBaseCoords agBaseCoords<-agBootstrapBlob agBootstrapBlobs agBootstrapCoords agClades agClades<-agCohesion agContinent agContinent<-agCoords agCoords<-agDates agDates<-agExtra agExtra<-agFill agFill<-agGroups agGroups<-agHomologousSr agIDs agIDs<-agLabIDs agLabIDs<-agLeverage agLineage agLineage<-agNames agNames<-agNucleotideSequences agNucleotideSequences<-agOpacity<-agOutline agOutline<-agOutlineWidth agOutlineWidth<-agPassage agPassage<-agReactivityAdjustments agReactivityAdjustments<-agReassortant agReassortant<-agReference agReference<-agRotation agRotation<-agSequences agSequences<-agShape agShape<-agShown agShown<-agSize agSize<-agStress agStressPerTiter agStrings agStrings<-agTriangulationBlob agTriangulationBlobs allMapDimensions allMapStresses applyMapTransform applyPlotspec as.json blob blobsize bootstrapBlobs bootstrapMap checkHemisphering colBases dilutionStepsize dilutionStepsize<-dimensionTestMap edit_agNames edit_srNames export_viewer fixedColBases fixedColBases<-getOptimization htmlAdjustedTiterTable htmlMergeReport htmlTiterTable keepBestOptimization keepOptimizations keepSingleOptimization layerNames layerNames<-listOptimizations logtiterTable logtiterTableLayers make.acmap mapBootstrap_agCoords mapBootstrap_srCoords mapCohesion mapComment mapComment<-mapDescription mapDescription<-mapDimensions mapDistances mapGadget mapName mapName<-mapRelaxed mapResiduals mapStress mapTransformation mapTransformation<-mapTranslation mapTranslation<-match_mapAntigens match_mapSera mergeMaps mergeReport minColBasis minColBasis<-moveTrappedPoints numAntigens numLayers numOptimizations numPoints numSera numSeraGroups optimizeAgReactivity optimizeMap orderAntigens orderSera plot_map_table_distance plotly_map_table_distance procrustesData procrustesMap ptBaseCoords ptBootstrapBlobs ptBootstrapCoords ptCoords ptCoords<-ptDrawingOrder ptDrawingOrder<-ptTriangulationBlobs RacMerge.options RacOptimizer.options RacViewer RacViewer.options RacViewerOutput randomizeCoords read.acmap read.titerTable realignMap realignOptimizations recalculateStress reflectMap relaxMap relaxMapOneStep removeAntigens removeOptimizations removeSera renderRacViewer rotateMap runGUI save.acmap save.coords save.titerTable setLegend sortOptimizations splitTiterLayers srAnnotations srAnnotations<-srAspect srAspect<-srBaseCoords srBaseCoords<-srBootstrapBlob srBootstrapBlobs srBootstrapCoords srClades srClades<-srCohesion srCoords srCoords<-srDates srDates<-srExtra srExtra<-srFill srFill<-srGroups srGroups<-srHomologousAgs srHomologousAgs<-srIDs srIDs<-srLeverage srLineage srLineage<-srNames srNames<-srNucleotideSequences srNucleotideSequences<-srOpacity<-srOutline srOutline<-srOutlineWidth srOutlineWidth<-srPassage srPassage<-srReassortant srReassortant<-srReference srReference<-srRotation srRotation<-srSequences srSequences<-srShape srShape<-srShown srShown<-srSize srSize<-srSpecies srSpecies<-srStress srStressPerTiter srStrings srStrings<-srTriangulationBlob srTriangulationBlobs standardizeStrainNames stressBlobs stressTable subsetMap tableColbases tableDistances titerLeverage titerTable titerTable<-titerTableLayers translateMap triangulationBlobs update_ferret_seraNames view

Dependencies:base64enc brotli bslib cachem cli colorspace commonmark cpp11 crayon digest dplyr ellipsis evaluate fansi farver fastmap FNN fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httpuv igraph isoband jquerylib jsonlite kernlab KernSmooth knitr ks labeling later lattice lifecycle magrittr MASS Matrix mclust memoise mgcv mime multicool munsell mvtnorm nlme pillar pkgconfig pracma promises R6 rapidjsonr rappdirs RColorBrewer Rcpp RcppArmadillo RcppEnsmallen RcppProgress rlang rmarchingcubes rmarkdown sass scales shape shiny shinyFiles shinyjs sourcetools tibble tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable yaml

Assessing map uncertainty

Rendered fromassessing_map_uncertainty.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-11-24
Started: 2023-09-04

Comparing maps

Rendered fromcomparing-maps.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-12-01
Started: 2023-09-04

Customising map appearance

Rendered fromcustomising-map-appearance.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-09-04
Started: 2023-09-04

Making an antigenic map from titer data

Rendered frommaking-a-map-from-scratch.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-12-01
Started: 2023-09-04

Merging maps

Rendered frommerging-maps.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-09-04
Started: 2023-09-04

Working with sequence data

Rendered fromadding-sequences.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-12-01
Started: 2023-09-04

Help page	Topics
Generate a new acmap object	acmap
Get acmap attributes	acmapAttributes numAntigens numLayers numOptimizations numPoints numSera numSeraGroups
Add a new optimization to an acmap object	addOptimization
Get the reactivity adjusted log titer table	adjustedLogTiterTable
Get the reactivity adjusted titer table	adjustedTiterTable
Getting and setting antigen attributes	agAttributes agContinent agContinent<- agDates agDates<- agExtra agExtra<- agIDs agIDs<- agLineage agLineage<- agNames agNames<- agPassage agPassage<- agReassortant agReassortant<- agReference agReference<- agStrings agStrings<-
Check map cohesion	agCohesion mapCohesion srCohesion
Getting and setting antigen groups	agGroups agGroups<-
Get homologous sera for each antigen	agHomologousSr
Getting and setting antigen lab id information	agLabIDs agLabIDs<-
Get and set antigen reactivity adjustments	agReactivityAdjustments agReactivityAdjustments<-
Getting and setting antigen sequence information	agNucleotideSequences agNucleotideSequences<- agSequences agSequences<-
Apply the current map transformation	applyMapTransform
Apply a plotspec from another acmap	applyPlotspec
Convert map to json format	as.json
Plot a blob object	blob
Calculate size of a blob object	blobsize
Calculate bootstrap blob data for an antigenic map	bootstrapBlobs
Perform a bootstrap on a map	bootstrapMap
Check for hemisphering or trapped points	checkHemisphering
Getting and setting column bases	colBases fixedColBases fixedColBases<- minColBasis minColBasis<-
Deprecated functions	deprecated_functions stressBlobs
Get or set the dilution stepsize associated with a map	dilutionStepsize dilutionStepsize<-
Perform dimension testing on a map object	dimensionTestMap
Edit antigen names in an acmap	edit_agNames
Edit sera names in an acmap	edit_srNames
Export the map viewer	export_viewer
Get optimization details from an acmap object	getOptimization
Plot an antigenic map using ggplot	ggplot.acmap
Return an html formatted titer table with antigen reactivity adjustments applied	htmlAdjustedTiterTable
Return an html formatted merge report	htmlMergeReport
Return an html formatted titer table	htmlTiterTable
Keep only the lowest stress map optimization	keepBestOptimization
Keep specified optimization runs	keepOptimizations
Keep only a single optimization run	keepSingleOptimization
Get and set map layer names	layerNames layerNames<-
Get all optimization details from an acmap object	listOptimizations
Get the log titers from an acmap	logtiterTable
Return a list of logtiter table layers	logtiterTableLayers
Make an antigenic map from scratch	make.acmap
Plot map vs table distances	map-table-distances plotly_map_table_distance plot_map_table_distance
Get bootstrap coordinates associated with a map	mapBootstrapCoords mapBootstrap_agCoords mapBootstrap_ptBaseCoords mapBootstrap_srCoords
Get or set an optimization run comment	mapComment mapComment<-
Getting and setting the map description	mapDescription mapDescription<-
Get the current map dimensions	mapDimensions
Return calculated map distances for an acmap	mapDistances
Open a shiny gadget to view the map	mapGadget
Getting and setting the map name	mapName mapName<-
Check if a map has been fully relaxed	mapRelaxed
Get a table of residuals from an acmap	mapResiduals
Calculate the current map stress	mapStress
Reading map transformation data	mapTransformation mapTransformation<- mapTranslation mapTranslation<-
Find matching antigens or sera between 2 maps	matchStrains match_mapAntigens match_mapSera
Merging maps	mergeMaps
Return a merge report	mergeReport
Move trapped points	moveTrappedPoints
Get optimization properties	allMapDimensions allMapStresses optimizationProperties
Optimize antigen reactivity adjustments	optimizeAgReactivity
Optimize an acmap	optimizeMap
Order antigens and sera	orderAntigens orderPoints orderSera
Plot an antigenic map	plot.acmap
Get individual point stress	agStress agStressPerTiter pointStress srStress srStressPerTiter
Return procrustes data on a map comparison	procrustesData
Return procrustes information	procrustesMap
Getting and setting point annotation information	agAnnotations agAnnotations<- ptAnnotations srAnnotations srAnnotations<-
Getting and setting base coordinates	agBaseCoords agBaseCoords<- ptBaseCoords srBaseCoords srBaseCoords<-
Get antigen or serum bootstrap blob information	agBootstrapBlob agBootstrapBlobs ptBootstrapBlob ptBootstrapBlobs srBootstrapBlob srBootstrapBlobs
Get antigen or serum bootstrap coordinates information	agBootstrapCoords ptBootstrapCoords srBootstrapCoords
Getting and setting point clade information	agClades agClades<- ptClades srClades srClades<-
Getting and setting point coordinates	agCoords agCoords<- ptCoords ptCoords<- srCoords srCoords<-
Get and set point drawing order in map	ptDrawingOrder ptDrawingOrder<-
Calculate point leverage	agLeverage ptLeverage srLeverage titerLeverage
Set point opacity in a map	agOpacity<- ptOpacity srOpacity<-
Getting and setting point plotting styles	agAspect 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 information	agTriangulationBlob agTriangulationBlobs ptTriangulationBlob ptTriangulationBlobs srTriangulationBlob srTriangulationBlobs
Set acmap merge options	RacMerge.options
Set acmap optimization options	RacOptimizer.options
Create a RacViewer widget	RacViewer
Shiny bindings for RacViewer	RacViewer-shiny RacViewerOutput renderRacViewer
Set viewer options	RacViewer.options
Randomize map coordinates	randomizeCoords
Read in acmap data from a file	read.acmap
Read in a table of titer data	read.titerTable
Realign map to match another	realignMap
Realigns optimizations in the map	realignOptimizations
Recalculate the stress associated with an acmap optimization	recalculateStress
Reflect a map	reflectMap
Relax a map	relaxMap
Relax a map one step in the optimiser	relaxMapOneStep
Remove map optimizations	removeOptimizations
Remove antigens and sera	removeAntigens removePoints removeSera
Rotate a map	rotateMap
Open the Racmacs GUI	runGUI
Save acmap data to a file	save.acmap
Save acmap coordinate data to a file	save.coords
Save titer data to a file	save.titerTable
Set acmap legend	setLegend
Sort optimizations by stress	sortOptimizations
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	splitTiterLayers
Getting and setting sera attributes	srAttributes srDates srDates<- srExtra srExtra<- srIDs srIDs<- srLineage srLineage<- srNames srNames<- srPassage srPassage<- srReassortant srReassortant<- srReference srReference<- srSpecies srSpecies<- srStrings srStrings<-
Getting and setting sera groups	srGroups srGroups<-
Get and set homologous antigens for sera	srHomologousAgs srHomologousAgs<-
Getting and setting sera sequence information	srNucleotideSequences srNucleotideSequences<- srSequences srSequences<-
Standardize strain names	standardizeStrainNames
Get a stress table from an acmap	stressTable
Remove antigens and sera	subsetCommonAgs subsetCommonPoints subsetCommonSrGroups
Subset an antigenic map	subsetMap
Calculate column bases for a titer table	tableColbases
Return calculated table distances for an acmap	tableDistances
Getting and setting map titers	titerTable titerTable<-
Getting and setting the flat titer table	titerTableFlat titerTableFlat<-
Getting and setting titer table layers	titerTableLayers titerTableLayers<-
Translate a map	translateMap
Calculate triangulation blobs data for an antigenic map	triangulationBlobs
Notes on unstable maps	unstableMaps
S3 method for viewing objects	view
Viewing racmap objects	view.acmap
Default method for viewing objects	view.default

Package: Racmacs 1.2.9

Racmacs: Antigenic Cartography Macros

Assessing map uncertainty

Comparing maps

Customising map appearance

Making an antigenic map from titer data

Merging maps

Working with sequence data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)