API for Racmacs
Antigenic Cartography Macros

Global functions
.onLoad Source code
RacMerge.options Man page Source code
RacOptimizer.options Man page Source code
RacViewer Man page Source code
RacViewer-shiny Man page
RacViewer.options Man page Source code
RacViewerOutput Man page Source code
Racmacs Man page
Racmacs-package Man page
`agAnnotations<-` Source code
`agClades<-` Source code
`agCoords<-` Source code
`agDiagnostics<-` Source code
`agFill<-` Source code
`agGroups<-` Source code
`agLabIDs<-` Source code
`agNucleotideSequences<-` Source code
`agOpacity<-` Source code
`agOutline<-` Source code
`agReactivityAdjustments<-` Source code
`agSequences<-` Source code
`dilutionStepsize<-` Source code
`layerNames<-` Source code
`mapDescription<-` Source code
`mapName<-` Source code
`ptCoords<-` Source code
`ptDrawingOrder<-` Source code
`srAnnotations<-` Source code
`srClades<-` Source code
`srCoords<-` Source code
`srDiagnostics<-` Source code
`srFill<-` Source code
`srGroups<-` Source code
`srHomologousAgs<-` Source code
`srNucleotideSequences<-` Source code
`srOpacity<-` Source code
`srOutline<-` Source code
`srSequences<-` Source code
`titerTable<-` Source code
`titerTableFlat<-` Source code
`titerTableLayers<-` Source code
ac_ag_get_annotations Source code
ac_ag_get_clade Source code
ac_ag_get_continent Source code
ac_ag_get_date Source code
ac_ag_get_extra Source code
ac_ag_get_group Source code
ac_ag_get_group_levels Source code
ac_ag_get_id Source code
ac_ag_get_labids Source code
ac_ag_get_lineage Source code
ac_ag_get_match_id Source code
ac_ag_get_name Source code
ac_ag_get_passage Source code
ac_ag_get_reassortant Source code
ac_ag_get_reference Source code
ac_ag_get_strings Source code
ac_ag_names Source code
ac_ag_set_annotations Source code
ac_ag_set_clade Source code
ac_ag_set_continent Source code
ac_ag_set_date Source code
ac_ag_set_extra Source code
ac_ag_set_group Source code
ac_ag_set_group_levels Source code
ac_ag_set_id Source code
ac_ag_set_labids Source code
ac_ag_set_lineage Source code
ac_ag_set_name Source code
ac_ag_set_passage Source code
ac_ag_set_reassortant Source code
ac_ag_set_reference Source code
ac_ag_set_strings Source code
ac_align_coords Source code
ac_align_map Source code
ac_align_optimization Source code
ac_align_optimizations Source code
ac_apply_optimization_transform Source code
ac_bootstrap_map Source code
ac_coordDistMatrix Source code
ac_coord_dists Source code
ac_coords_stress Source code
ac_dimension_test_map Source code
ac_errorline_data Source code
ac_get_ag_coords Source code
ac_get_sr_coords Source code
ac_hemi_test Source code
ac_match_map_ags Source code
ac_match_map_sr Source code
ac_merge_frozen_merge Source code
ac_merge_frozen_overlay Source code
ac_merge_incremental Source code
ac_merge_relaxed_overlay Source code
ac_merge_reoptimized Source code
ac_merge_tables Source code
ac_merge_titer_layers Source code
ac_merge_titers Source code
ac_move_trapped_points Source code
ac_newOptimization Source code
ac_new_antigen Source code
ac_new_serum Source code
ac_numeric_table_distances Source code
ac_opt_get_ag_base_coords Source code
ac_opt_get_agreactivityadjustments Source code
ac_opt_get_comment Source code
ac_opt_get_dimensions Source code
ac_opt_get_fixedcolbases Source code
ac_opt_get_mincolbasis Source code
ac_opt_get_sr_base_coords Source code
ac_opt_get_stress Source code
ac_opt_get_transformation Source code
ac_opt_get_translation Source code
ac_opt_set_ag_base_coords Source code
ac_opt_set_agreactivityadjustments Source code
ac_opt_set_comment Source code
ac_opt_set_fixedcolbases Source code
ac_opt_set_mincolbasis Source code
ac_opt_set_sr_base_coords Source code
ac_opt_set_stress Source code
ac_opt_set_transformation Source code
ac_opt_set_translation Source code
ac_optimize_map Source code
ac_plotspec_get_aspect Source code
ac_plotspec_get_fill Source code
ac_plotspec_get_outline Source code
ac_plotspec_get_outline_width Source code
ac_plotspec_get_rotation Source code
ac_plotspec_get_shape Source code
ac_plotspec_get_shown Source code
ac_plotspec_get_size Source code
ac_plotspec_set_aspect Source code
ac_plotspec_set_fill Source code
ac_plotspec_set_outline Source code
ac_plotspec_set_outline_width Source code
ac_plotspec_set_rotation Source code
ac_plotspec_set_shape Source code
ac_plotspec_set_shown Source code
ac_plotspec_set_size Source code
ac_point_residuals Source code
ac_point_stresses Source code
ac_procrustes Source code
ac_procrustes_map_coords Source code
ac_procrustes_map_data Source code
ac_progress_bar Source code
ac_reactivity_adjustment_stress Source code
ac_reflect_optimization Source code
ac_relaxOptimization Source code
ac_relax_coords Source code
ac_rotate_optimization Source code
ac_runOptimizations Source code
ac_set_ag_coords Source code
ac_set_sr_coords Source code
ac_sr_get_annotations Source code
ac_sr_get_clade Source code
ac_sr_get_continent Source code
ac_sr_get_date Source code
ac_sr_get_extra Source code
ac_sr_get_group Source code
ac_sr_get_group_levels Source code
ac_sr_get_homologous_ags Source code
ac_sr_get_id Source code
ac_sr_get_lineage Source code
ac_sr_get_match_id Source code
ac_sr_get_name Source code
ac_sr_get_passage Source code
ac_sr_get_reassortant Source code
ac_sr_get_reference Source code
ac_sr_get_species Source code
ac_sr_get_strings Source code
ac_sr_set_annotations Source code
ac_sr_set_clade Source code
ac_sr_set_continent Source code
ac_sr_set_date Source code
ac_sr_set_extra Source code
ac_sr_set_group Source code
ac_sr_set_group_levels Source code
ac_sr_set_homologous_ags Source code
ac_sr_set_id Source code
ac_sr_set_lineage Source code
ac_sr_set_name Source code
ac_sr_set_passage Source code
ac_sr_set_reassortant Source code
ac_sr_set_reference Source code
ac_sr_set_species Source code
ac_sr_set_strings Source code
ac_stress_blob_grid Source code
ac_subset_map Source code
ac_table_colbases Source code
ac_titer_layer_merge_types Source code
ac_titer_layer_sd Source code
ac_titer_merge_type Source code
ac_translate_optimization Source code
ac_update_progress Source code
acmap Man page Source code
acmap.new Source code
acmapAttributes Man page
acmap_to_json Source code
acpoint_grob Source code
addMapGrid Source code
addOptimization Man page Source code
adjustedLogTiterTable Man page Source code
adjustedTiterTable Man page Source code
agAnnotations Man page Source code
agAnnotations<- Man page
agAspect Man page
agAspect<- Man page
agAttributes Man page
agBaseBlob Source code
agBaseBootstrapBlobs Source code
agBaseCoords Man page
agBaseCoords<- Man page
agBaseTriangulationBlobs Source code
agBlob Source code
agBootstrapBlob Man page Source code
agBootstrapBlobs Man page Source code
agBootstrapCoords Man page Source code
agClades Man page Source code
agClades<- Man page
agCohesion Man page Source code
agContinent Man page
agContinent<- Man page
agCoords Man page Source code
agCoords<- Man page
agDates Man page
agDates<- Man page
agDiagnostics Source code
agExtra Man page
agExtra<- Man page
agExtraMatrix Source code
agFill Man page
agFill<- Man page
agGroupMatrix Source code
agGroups Man page Source code
agGroups<- Man page
agHemisphering Source code
agHomologousSr Man page Source code
agIDs Man page
agIDs<- Man page
agLabIDs Man page Source code
agLabIDs<- Man page
agLeverage Man page Source code
agLineage Man page
agLineage<- Man page
agMeanResiduals Source code
agNameMatrix Source code
agNames Man page
agNames<- Man page
agNucleotideSequences Man page Source code
agNucleotideSequences<- Man page
agNumMatrix Source code
agOpacity<- Man page
agOutline Man page
agOutline<- Man page
agOutlineWidth Man page
agOutlineWidth<- Man page
agPassage Man page
agPassage<- Man page
agReactivityAdjustments Man page Source code
agReactivityAdjustments<- Man page
agReassortant Man page
agReassortant<- Man page
agReference Man page
agReference<- Man page
agRotation Man page
agRotation<- Man page
agSequences Man page Source code
agSequences<- Man page
agShape Man page
agShape<- Man page
agShown Man page
agShown<- Man page
agSize Man page
agSize<- Man page
agStress Man page Source code
agStressPerTiter Man page Source code
agStrings Man page
agStrings<- Man page
agTriangulationBlob Man page Source code
agTriangulationBlobs Man page Source code
allMapDimensions Man page Source code
allMapProperties Source code
allMapStresses Man page Source code
antigens_getter Source code
antigens_setter Source code
applyMapTransform Man page Source code
applyPlotspec Man page Source code
as.json Man page Source code
as.plotly Source code
blob Man page Source code
blob_area Source code
blob_volume Source code
blobsize Man page Source code
bootstrapBlobs Man page Source code
bootstrapData Source code
bootstrapMap Man page Source code
btn_img Source code
calc_agLeverage Source code
calc_srLeverage Source code
calc_titerLeverage Source code
check.acmap Source code
check.charactermatrix Source code
check.charactervector Source code
check.dimensions Source code
check.integer Source code
check.integerlist Source code
check.logical Source code
check.logicalvector Source code
check.numeric Source code
check.numericmatrix Source code
check.numericvector Source code
check.optnum Source code
check.string Source code
check.validtiters Source code
checkHemisphering Man page Source code
clamp Source code
colBaseMatrix Source code
colBases Man page Source code
contour_blob Source code
convert3Dto2DrotationMatrix Source code
convertSelectedPoints Source code
coordDensityBlob Source code
coord_lims Source code
data2json Source code
deprecated_fn Source code
deprecated_functions Man page
dilutionStepsize Man page Source code
dilutionStepsize<- Man page
dimensionTestMap Man page Source code
dimtest_summary Source code
drawDetails.acpoint Source code
edit_agNames Man page Source code
edit_srNames Man page Source code
eulerFromMatrix Source code
expand_lims Source code
export.plot.test Source code
export.plotly.test Source code
export.viewer.test Source code
export_viewer Man page Source code
fixedColBases Man page
fixedColBases<- Man page
format_titers Source code
geom_acpoint Source code
getOptimization Man page Source code
get_ag_indices Source code
get_col_opacity Source code
get_pts_sequence_matrix Source code
get_sr_indices Source code
ggplot.acmap Man page Source code
ggplot_theme Source code
group_cols Source code
hasBootstrapBlobs Source code
hasBootstrapData Source code
hasHemisphering Source code
hasProcrustes Source code
hasTriangulationBlobs Source code
hist_ggplot Source code
htmlAdjustedTiterTable Man page Source code
htmlMergeReport Man page Source code
htmlTiterTable Man page Source code
html_titer_table Source code
interp2d Source code
is.wholenumber Source code
json_to_acmap Source code
keepBestOptimization Man page Source code
keepOptimizations Man page Source code
keepSingleOptimization Man page Source code
layerNames Man page Source code
layerNames<- Man page
list2matrix Source code
listOptimizations Man page Source code
log_titers Source code
logtiterTable Man page Source code
logtiterTableLayers Man page Source code
longAgData Source code
longMapData Source code
longSrData Source code
longTiterData Source code
lowerDrawingOrder Source code
make.acmap Man page Source code
make_html_legend Source code
make_titers Source code
map-table-distances Man page
mapBootstrapCoords Man page
mapBootstrap_agBaseCoords Source code
mapBootstrap_agCoords Man page Source code
mapBootstrap_ptBaseCoords Man page Source code
mapBootstrap_ptCoords Source code
mapBootstrap_srBaseCoords Source code
mapBootstrap_srCoords Man page Source code
mapCohesion Man page Source code
mapComment Man page
mapComment<- Man page
mapConnectivityDistances Source code
mapConnectivityGraph Source code
mapDescription Man page Source code
mapDescription<- Man page
mapDimensions Man page
mapDisconnected Source code
mapDistances Man page Source code
mapGUI Source code
mapGUI_server Source code
mapGUI_ui Source code
mapGadget Man page Source code
mapLims Source code
mapName Man page Source code
mapName<- Man page
mapPlotLims Source code
mapPoints Source code
mapRelaxed Man page Source code
mapResiduals Man page Source code
mapStress Man page Source code
mapTransformation Man page
mapTransformation<- Man page
mapTranslation Man page
mapTranslation<- Man page
matchStrains Man page
match_mapAntigens Man page Source code
match_mapSera Man page Source code
matrixFromEuler Source code
mergeMaps Man page Source code
mergeReport Man page Source code
mesh_volume Source code
minColBasis Man page
minColBasis<- Man page
moveTrappedPoints Man page Source code
numAntigens Man page Source code
numLayers Man page Source code
numOptimizations Man page Source code
numPoints Man page Source code
numSera Man page Source code
numSeraGroups Man page Source code
numeric_min_tabledists Source code
numeric_titers Source code
numerictiterTable Source code
optimizationProperties Man page
optimization_getter Source code
optimization_setter Source code
optimizeAgReactivity Man page Source code
optimizeMap Man page Source code
orderAntigens Man page Source code
orderPoints Man page
orderSera Man page Source code
package_required Source code
parallel_mode Source code
plot.acmap Man page Source code
plot_agMeanResiduals Source code
plot_agStressPerTiter Source code
plot_lims Source code
plot_map_table_distance Man page Source code
plot_srMeanResiduals Source code
plot_srStressPerTiter Source code
plot_sr_titers Source code
plotly_agMeanResiduals Source code
plotly_agStressPerTiter Source code
plotly_map_table_distance Man page Source code
plotly_srMeanResiduals Source code
plotly_srStressPerTiter Source code
plotly_sr_titers Source code
plotlyfn Source code
plotspec_getter Source code
plotspec_setter Source code
pointStress Man page
polygon_area Source code
postDrawDetails.acpoint Source code
preDrawDetails.acpoint Source code
print.Rac_html_merge_report Source code
print.acmap Source code
procrustesData Man page Source code
procrustesMap Man page Source code
ptAnnotations Man page
ptBaseBootstrapBlobs Source code
ptBaseCoords Man page Source code
ptBaseTriangulationBlobs Source code
ptBootstrapBlob Man page
ptBootstrapBlobs Man page Source code
ptBootstrapCoords Man page Source code
ptClades Man page
ptCoords Man page Source code
ptCoords<- Man page
ptDiagnostics Source code
ptDrawingOrder Man page Source code
ptDrawingOrder<- Man page
ptHemisphering Source code
ptLeverage Man page
ptOpacity Man page
ptProcrustes Source code
ptStyles Man page
ptTriangulationBlob Man page
ptTriangulationBlobs Man page Source code
randomizeCoords Man page Source code
rbind_list_to_matrix Source code
reactivity_adjust_titers Source code
read.acmap Man page Source code
read.titerTable Man page Source code
read_brotli Source code
realignMap Man page Source code
realignOptimizations Man page Source code
recalculateStress Man page Source code
reduce_matrix_dimensions Source code
reflectMap Man page Source code
reflect_coords_in_axis Source code
relaxMap Man page Source code
relaxMapOneStep Man page Source code
removeAntigens Man page Source code
removeOptimizations Man page Source code
removePoints Man page
removeSera Man page Source code
renderRacViewer Man page Source code
reqOptimizations Source code
reqRelaxed Source code
rotateMap Man page Source code
rotate_coords_by_degrees Source code
rotate_coords_by_radians Source code
rotation_matrix_2D Source code
rotation_matrix_3D Source code
roxygen_tags Source code
runDimensionTestMap Source code
runGUI Man page Source code
save.acmap Man page Source code
save.coords Man page Source code
save.titerTable Man page Source code
separate_meshes Source code
sera_getter Source code
sera_setter Source code
server_alignOptimizations Source code
server_checkHemisphering Source code
server_coordsChanged Source code
server_loadMapData Source code
server_loadPointStyleData Source code
server_loadTableData Source code
server_moveTrappedPoints Source code
server_optimizationChanged Source code
server_procrustesMap Source code
server_randomizeMap Source code
server_reflectMap Source code
server_relaxMap Source code
server_relaxMapOneStep Source code
server_removeOptimizations Source code
server_runOptimizations Source code
server_saveCoordsData Source code
server_saveMapData Source code
server_saveTableData Source code
server_triangulationBlobs Source code
setLegend Man page Source code
set_col_opacity Source code
set_pts_sequence_matrix Source code
setup_acmap Source code
simpleCap Source code
singleline Source code
sortOptimizations Man page Source code
splitTiterLayers Man page Source code
srAnnotations Man page Source code
srAnnotations<- Man page
srAspect Man page
srAspect<- Man page
srAttributes Man page
srBaseBlob Source code
srBaseBootstrapBlobs Source code
srBaseCoords Man page
srBaseCoords<- Man page
srBaseTriangulationBlobs Source code
srBlob Source code
srBootstrapBlob Man page Source code
srBootstrapBlobs Man page Source code
srBootstrapCoords Man page Source code
srClades Man page Source code
srClades<- Man page
srCohesion Man page Source code
srCoords Man page Source code
srCoords<- Man page
srDates Man page
srDates<- Man page
srDiagnostics Source code
srExtra Man page
srExtra<- Man page
srExtraMatrix Source code
srFill Man page
srFill<- Man page
srGroupMatrix Source code
srGroupOutline Source code
srGroups Man page Source code
srGroups<- Man page
srHemisphering Source code
srHomologousAgs Man page Source code
srHomologousAgs<- Man page
srHomologousAgsReindexed Source code
srIDs Man page
srIDs<- Man page
srLeverage Man page Source code
srLineage Man page
srLineage<- Man page
srMeanResiduals Source code
srNameMatrix Source code
srNames Man page
srNames<- Man page
srNucleotideSequences Man page Source code
srNucleotideSequences<- Man page
srNumMatrix Source code
srOpacity<- Man page
srOutline Man page
srOutline<- Man page
srOutlineWidth Man page
srOutlineWidth<- Man page
srPassage Man page
srPassage<- Man page
srReassortant Man page
srReassortant<- Man page
srReference Man page
srReference<- Man page
srRotation Man page
srRotation<- Man page
srSequences Man page Source code
srSequences<- Man page
srShape Man page
srShape<- Man page
srShown Man page
srShown<- Man page
srSize Man page
srSize<- Man page
srSpecies Man page
srSpecies<- Man page
srStress Man page Source code
srStressPerTiter Man page Source code
srStrings Man page
srStrings<- Man page
srTriangulationBlob Man page Source code
srTriangulationBlobs Man page Source code
standardizeStrainName Source code
standardizeStrainNames Man page Source code
strain_list_error Source code
strain_list_warning Source code
stressBlobs Man page
stressTable Man page Source code
subsetAntigens Source code
subsetCommonAgs Man page Source code
subsetCommonPoints Man page
subsetCommonSrGroups Man page Source code
subsetMap Man page Source code
subsetSera Source code
tab_img Source code
tableColbases Man page Source code
tableDistances Man page Source code
table_arg_deprecated Source code
titerLeverage Man page Source code
titerTable Man page Source code
titerTable<- Man page
titerTableFlat Man page Source code
titerTableFlat<- Man page
titerTableLayers Man page Source code
titerTableLayers<- Man page
titer_types_int Source code
titertypesTable Source code
titertypesTableLayers Source code
transformMapBlob Source code
translateMap Man page Source code
translate_coords Source code
triangulationBlobs Man page Source code
unstableMaps Man page
update_ferret_seraNames Man page Source code
validate_colors Source code
view Man page Source code
view.acmap Man page Source code
view.default Man page Source code
vmessage Source code
warn_disconnected Source code
warn_underconstrained Source code
Racmacs documentation built on June 22, 2024, 11:33 a.m.