Man pages for Racmacs
Antigenic Cartography Macros
| 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 |
| agAttributes | Getting and setting antigen attributes |
| agGroups | Getting and setting antigen groups |
| agHomologousSr | Get homologous sera for each antigen |
| agLabIDs | Getting and setting antigen lab id information |
| agReactivityAdjustments | Get and set antigen reactivity adjustments |
| agSequences | Getting and setting antigen sequence information |
| applyMapTransform | Apply the current map transformation |
| applyPlotspec | Apply a plotspec from another acmap |
| as.json | Convert map to json format |
| 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 |
| checkHemisphering | Check for hemisphering or trapped points |
| colBases | Getting and setting column bases |
| deprecated_functions | Deprecated functions |
| dilutionStepsize | Get or set the dilution stepsize associated with a map |
| dimensionTestMap | Perform dimension testing on a map object |
| edit_agNames | Edit antigen names in an acmap |
| edit_srNames | Edit sera names in an acmap |
| export_viewer | Export the map viewer |
| getOptimization | Get optimization details from an acmap object |
| ggplot.acmap | Plot an antigenic map using ggplot |
| htmlAdjustedTiterTable | Return an html formatted titer table with antigen reactivity... |
| htmlMergeReport | Return an html formatted merge report |
| htmlTiterTable | Return an html formatted titer table |
| keepBestOptimization | Keep only the lowest stress map optimization |
| keepOptimizations | Keep specified optimization runs |
| keepSingleOptimization | Keep only a single optimization run |
| 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 |
| make.acmap | Make an antigenic map from scratch |
| mapBootstrapCoords | Get bootstrap coordinates associated with a map |
| mapCohesion | Check map cohesion |
| mapComment | Get or set an optimization run comment |
| 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 |
| mapRelaxed | Check if a map has been fully relaxed |
| mapResiduals | Get a table of residuals from an acmap |
| mapStress | Calculate the current map stress |
| map-table-distances | Plot map vs table distances |
| mapTransformation | Reading map transformation data |
| matchStrains | Find matching antigens or sera between 2 maps |
| mergeMaps | Merging maps |
| mergeReport | Return a merge report |
| moveTrappedPoints | Move trapped points |
| optimizationProperties | Get optimization properties |
| optimizeAgReactivity | Optimize antigen reactivity adjustments |
| optimizeMap | Optimize an acmap |
| orderPoints | Order antigens and sera |
| plot.acmap | Plot an antigenic map |
| 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 |
| ptBootstrapCoords | Get antigen or serum bootstrap coordinates information |
| ptClades | Getting and setting point clade information |
| ptCoords | Getting and setting point coordinates |
| 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 |
| Racmacs-package | Racmacs: Antigenic Cartography Macros |
| RacMerge.options | Set acmap merge options |
| RacOptimizer.options | Set acmap optimization options |
| RacViewer | Create a RacViewer widget |
| RacViewer.options | Set viewer options |
| RacViewer-shiny | 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 |
| removeOptimizations | Remove map optimizations |
| removePoints | Remove antigens and sera |
| rotateMap | Rotate a map |
| runGUI | Open the Racmacs GUI |
| 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... |
| srAttributes | Getting and setting sera attributes |
| srGroups | Getting and setting sera groups |
| srHomologousAgs | Get and set homologous antigens for sera |
| srSequences | Getting and setting sera sequence information |
| standardizeStrainNames | Standardize strain names |
| stressTable | Get a stress table from an acmap |
| subsetCommonPoints | Remove antigens and sera |
| subsetMap | Subset an antigenic map |
| tableColbases | Calculate column bases for a titer table |
| tableDistances | Return calculated table distances for an acmap |
| titerTable | Getting and setting map titers |
| titerTableFlat | Getting and setting the flat titer table |
| titerTableLayers | Getting and setting titer table layers |
| translateMap | Translate a map |
| triangulationBlobs | Calculate triangulation blobs data for an antigenic map |
| unstableMaps | Notes on unstable maps |
| update_ferret_seraNames | Update the ferret serum names to match antigens |
| view | S3 method for viewing objects |
| view.acmap | Viewing racmap objects |
| view.default | Default method for viewing objects |
