| Add an Axis to an NG-CHM Version 2 | + +,ngchmVersion2,ngchmAxis-method |
| Provide a simpler method for accessing repo methods | $.shaidyRepo |
| Helper function to cast variables as integers. | castAsInteger |
| Helper function to cast list as integer | castListAsInteger |
| Add a list of objects to a NGCHM. | chmAdd chmAdd,ngchm-method |
| Add an axis type to a NGCHM. | chmAddAxisType chmAddAxisType,ngchm,character,character,character-method chmAddAxisType,ngchm,character,character,missing-method chmAddAxisType,ngchm,character,character,ngchmJS-method |
| Add a colormap to a NGCHM. | chmAddColormap chmAddColormap,ngchm,ngchmColormap-method |
| Add a covariate to an auxiliary dataset. | chmAddCovariate chmAddCovariate,ngchmDataset,character,ngchmCovariate-method |
| Add a covariate bar to a NGCHM. | chmAddCovariateBar chmAddCovariateBar,ngchm,character,list-method chmAddCovariateBar,ngchm,character,ngchmBar-method chmAddCovariateBar,ngchm,character,ngchmCovariate-method chmAddCovariateBar,ngchm,character,ngchmCovariateBar-method |
| Add custom CSS to a NGCHM. | chmAddCSS chmAddCSS,ngchm,character,character-method chmAddCSS,ngchm,character-method |
| Add an auxiliary dataset to a NGCHM. | chmAddDataset chmAddDataset,ngchm,ngchmDataset-method |
| Add an extra dialog to a NGCHM. | chmAddDialog chmAddDialog,ngchm,ngchmDialog-method |
| Add a Layer to a NGCHM. | chmAddLayer chmAddLayer,ngchm,matrix-method chmAddLayer,ngchm,ngchmLayer-method |
| Add a menu entry to a NGCHM. | chmAddMenuItem chmAddMenuItem,ngchm,character,character,character-method chmAddMenuItem,ngchm,character,character,ngchmJS-method |
| Add MetaData to NG-CHM | chmAddMetaData chmAddMetaData,ngchm,character,character,character-method |
| Generate an overview image of the NGCHM when making it. | chmAddOverview chmAddOverview,ngchm,character,numeric,numeric-method chmAddOverview,ngchm,character,optNumeric,optNumeric-method |
| Add PCA coordinates to an NG-CHM. | chmAddPCA |
| Add custom property to a NGCHM. | chmAddProperty chmAddProperty,ngchm,character,character-method |
| Add reduced dimension coordinates to an NG-CHM. | chmAddReducedDim |
| Add a link to related information to the NGCHM. | chmAddRelated chmAddRelated,ngchm,character,character,character-method |
| Add a group of related links to the NGCHM. | chmAddRelatedGroup chmAddRelatedGroup,ngchm,character,character,character,character-method chmAddRelatedGroup,ngchm,character,character,character,missing-method |
| Add a CHM-specific axis type function to a NGCHM. | chmAddSpecificAxisTypeFunction chmAddSpecificAxisTypeFunction,ngchm,character,character,character,character-method chmAddSpecificAxisTypeFunction,ngchm,character,character,character,ngchmJS-method |
| Add tags to a NGCHM. | chmAddTag chmAddTag,ngchm,character,character-method chmAddTag,ngchm,character-method |
| Add a file template to the NGCHM. | chmAddTemplate chmAddTemplate,ngchm,charOrFunction,character,optList-method |
| Add standard toolbox to an NG-CHM axis | chmAddToolboxR chmAddToolboxR,ngchm,character,character,character,character-method |
| Add Toolbox R2 to NG-CHM | chmAddToolboxR2 chmAddToolboxR2,ngchm,character,character,character-method |
| Add Toolbox RC to NG-CHM | chmAddToolboxRC chmAddToolboxRC,ngchm,character,character,character,character-method chmAddToolboxRC,ngchm,character,character,character-method |
| Add TSNE coordinates to an NG-CHM. | chmAddTSNE |
| Add UMAP coordinates to an NG-CHM. | chmAddUMAP |
| Add UWOT::UMAP coordinates to an NG-CHM. | chmAddUWOT |
| Create a new Axis for adding to an NG-CHM. | chmAxis |
| Create a new AxisType for adding to an ngchmAxis. | chmAxisType |
| Bind values to an existing JS function. | chmBindFunction chmBindFunction,character,character,list-method chmBindFunction,character,ngchmJS,list-method |
| Browse the NGCHMs on the specified server in the viewer. | chmBrowse |
| Set the column order of data shown in a NGCHM. | chmColOrder<- chmColOrder<-,ngchm,optDendrogram-method |
| Get the color map of an NG-CHM object. | chmColorMap |
| Set the color map of an NG-CHM object | chmColorMap<- |
| Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate. | chmColors |
| Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate. | chmColors<- |
| Get a covariate attached to an NG-CHM dataset. | chmCovariate |
| Get a covariate bar attached to an NG-CHM. | chmCovariateBar |
| Create a new NG-CHM Collection | chmCreateCollection |
| Create an ngchmServer object for a managed NG-CHM server | chmCreateManagedServer |
| Create an ngchmServer object from a specification. | chmCreateServer |
| Get the user's current collection | chmCurrentCollection |
| Get the user's current server | chmCurrentServer |
| Return default column order of an NGCHM | chmDefaultColOrder |
| Return default row order of an NGCHM | chmDefaultRowOrder |
| Get the name of a NGCHM server. | chmDeployServer chmDeployServer,ngchmServer-method |
| Export a standalone NGCHM to a file. | chmExportToFile |
| Export a standalone HTML containing the NGCHM to a file. | chmExportToHTML |
| Export a PDF of the NGCHM to a file. | chmExportToPDF |
| Get Javascript function name for accessing a specific string field in each element of string vector. | chmFieldAccessFunction |
| Get the dataset from an NG-CHM object | chmGetDataset chmGetDataset,ngchmLayer-method |
| Get per-user configuration for a specific deploy Server. | chmGetDeployServerConfig |
| Get a predefined Javascript function for use in NGCHM menus | chmGetFunction |
| Get the file path to the specified overview file. | chmGetOverview |
| Get Property from NG-CHM | chmGetProperty chmGetProperty,ngchmVersion2,character-method chmGetProperty,ngchmVersion2-method |
| Get information about a type name. | chmGetTypeInfo |
| Get the URL for an installed NGCHM. | chmGetURL chmGetURL,character-method chmGetURL,ngchm-method |
| Determine if the NG-CHM has the given property. | chmHasProperty chmHasProperty,ngchmVersion2,character-method chmHasProperty,ngchmVersion2-method |
| Add an NG-CHM to an NG-CHM collection. | chmInstall chmInstall,ngchm-method |
| Get the label/name of an NG-CHM object. | chmLabel |
| Set the label/name of an NG-CHM object | chmLabel<- |
| Get a specified Data Layer from an NG-CHM. | chmLayer |
| Set (or append) a specified Data Layer in an NG-CHM. | chmLayer<- |
| List the predefined Javascript functions available for use in NGCHM menus. | chmListFunctions |
| List NG-CHM Servers | chmListServers |
| List known axis types. | chmListTypes |
| Load CHM from NG-CHM server | chmLoadCHM chmLoadCHM,character,character-method chmLoadCHM,character,missing-method chmLoadCHM,ngchmServer,character-method |
| Load an NG-CHM from an NG-CHM server. | chmLoadShaidyCHM |
| Compile a NGCHM. | chmMake chmMake,ngchm-method |
| Make NG-CHM Private on Server | chmMakePrivate chmMakePrivate,character,character-method chmMakePrivate,character,ngchm-method chmMakePrivate,ngchmServer,character-method chmMakePrivate,ngchmServer,ngchm-method |
| Make NG-CHM Public on Server | chmMakePublic chmMakePublic,character,character-method chmMakePublic,character,ngchm-method chmMakePublic,ngchmServer,character-method chmMakePublic,ngchmServer,ngchm-method |
| Open the NG-CHM Manager | chmManager |
| Get the name of a NGCHM. | chmName chmName,ngchm-method |
| Create a new NGCHM. | chmNew |
| Create a new Color Map for use in constructing a NGCHM | chmNewColorMap |
| Create a new Covariate for adding to an NGCHM auxilary dataset. | chmNewCovariate |
| Create a new covariate Bar for a NGCHM | chmNewCovariateBar |
| Create a new Data Layer for a NGCHM. | chmNewDataLayer |
| Create a new Dataset for a NGCHM. | chmNewDataset |
| Create a new Dialog for a NGCHM. | chmNewDialog |
| Create a new Javascript function for adding to a NGCHM menu. | chmNewFunction |
| Create a new Property for adding to a NGCHM. | chmNewProperty |
| Create a new object representing a NGCHM server. | chmNewServer |
| Return original column order of an NGCHM | chmOriginalColOrder |
| Return original row order of an NGCHM | chmOriginalRowOrder |
| Create NG-CHM Properties | chmProperties |
| Get the value of an NG-CHM property. | chmProperty |
| Set the value of an NG-CHM property. | chmProperty<- |
| Return random column order of an NGCHM | chmRandomColOrder |
| Return random row order of an NGCHM | chmRandomRowOrder |
| Register a predefined Javascript function for use in NGCHM Axis menus. | chmRegisterAxisFunction |
| Register a predefined Javascript function for use in NGCHM menus. | chmRegisterFunction |
| Define and register a Javascript function for obtaining a specific metadata value. | chmRegisterGetMetadataFunction |
| Register a predefined Javascript function for use in NGCHM Matrix menus. | chmRegisterMatrixFunction |
| Register a Javascript function for use in the NGCHM toolbox. | chmRegisterToolboxFunction |
| Register a type name. | chmRegisterType |
| Register a predefined Javascript function for converting values from one type to another. | chmRegisterTypeMapper |
| Define and register a Javascript function for converting a lists of type values into single values. | chmRegisterTypeSplitter |
| Set the row order of data shown in a NGCHM. | chmRowOrder<- chmRowOrder<-,ngchm,optDendrogram-method |
| Get a registered ngchmServer object for use in making and installing NGCHMs | chmServer |
| Set the user's current server and/or collection | chmSetCollection |
| Set Access Credentials for NG-CHM Server | chmSetCredentials chmSetCredentials,character,character-method chmSetCredentials,ngchmServer,character-method |
| Specify per-user configuration for a specific deploy Server. | chmSetDeployServerConfig |
| Get Javascript function name for performing a specific string operation on each element of a string vector. | chmStringopFunction |
| Creates new treeCuts object | chmTreeGaps |
| Remove an NG-CHM from Server | chmUninstall chmUninstall,character-method chmUninstall,ngchm-method |
| Get the base URL for a NGCHM installed on a NGCHM server. | chmUrlBase chmUrlBase,ngchmServer-method |
| Output Javascript code required to customize an NGCHM. | chmWriteCustomJS |
| Generic method to get a dimensions matrix from obj. | getDimensions getDimensions,prcomp getDimensions,Seurat getDimensions,umap getDimensions.default getDimensions.prcomp getDimensions.Seurat getDimensions.umap |
| Obtain the git hash of an existing file. | gitHashObject |
| Initialize Logging | initLogging |
| Next Generation Clustered Heat Map (NGCHM) Construction Library | NGCHM-package NGCHM |
| Class representing a Next Generation Clustered Heat Map (NGCHM) under construction. | ngchm-class |
| Javascript extensions for the Next Generation Clustered Heat Map (NGCHM) Construction Library | NGCHM-functions |
| Initialization of the NGCHM library. | NGCHM-initialization |
| Add a data file to a local shaidy repository | ngchmAddDatasetBlob |
| Add a matrix reference to a collection | ngchmAddMatrixToCollection |
| Add an object reference to a collection | ngchmAddObjectToCollection |
| Class representing an axis of a Next Generation Clustered Heat Map (NG-CHM). | ngchmAxis-class |
| Class representing an axis function for Next Generation Clustered Heat Map (NGCHM). | ngchmAxisFunction-class |
| Class representing a type attached to an axis in a Next Generation Clustered Heat Map (NGCHM). | ngchmAxisType-class |
| Class representing a Covariate Bar on a Next Generation Clustered Heat Map (NGCHM). | ngchmBar-class |
| Recursively determine if collection uuid is contained in collection A collecton always contains itself. | ngchmCollectionInCollection |
| Create a recursive description of a collection | ngchmCollectionTree |
| Class representing a Color Map on a Next Generation Clustered Heat Map (NGCHM). | ngchmColormap-class |
| Class representing a Covariate attached to a Dataset | ngchmCovariate-class |
| Create and register an NGCHM server protocol implementation. | ngchmCreateServerProtocol |
| Class representing custom CSS for a Next Generation Clustered Heat Map (NGCHM). | ngchmCSS-class |
| Class representing a Dataset attached to a NGCHM | ngchmDataset-class |
| Class representing an addon dialog | ngchmDialog-class |
| Find a repository, if any, that contains the requested shaid | ngchmFindRepo |
| Compute shaid for a data file | ngchmGetDataFileShaid |
| Get the ngchm environment (for debugging only). | ngchmGetEnv |
| Get a HTTR handle for the server's view/WS URL | ngchmGetHandleHTTR |
| Get the axis labels of a shaidy dataset or dendrogram | ngchmGetLabels |
| Get the axis labels of a shaidy dataset or dendrogram | ngchmGetLabelsStr |
| Get Protocol Parameter for NG-CHM Server | ngchmGetProtoParam |
| Get Server Protocol for NG-CHM | ngchmGetServerProtocol |
| Initialize Shaidy Repository for NG-CHM | ngchmInitShaidyRepository |
| Class representing a custom Javascript function for a Next Generation Clustered Heat Map (NGCHM). | ngchmJS-class |
| Class representing a Layer on a Next Generation Clustered Heat Map (NGCHM). | ngchmLayer-class |
| List defined server protocols | ngchmListServerProtocols |
| Load a data matrix from a local shaidy repository | ngchmLoadDatasetBlob |
| Make an original format NGCHM. | ngchmMakeFormat.original |
| Make a shaidy format NGCHM. | ngchmMakeFormat.shaidy |
| Class representing a matrix function for Next Generation Clustered Heat Map (NGCHM). | ngchmMatrixFunction-class |
| Class representing a Menu Item for a Next Generation Clustered Heat Map (NGCHM). | ngchmMenuItem-class |
| Class representing meta data attached to an NG-CHM | ngchmMetaData-class |
| Create a new Classification Bar for a NGCHM | ngchmNewBar |
| Create a new collection in a local shaidy repository | ngchmNewCollection |
| Class representing an overview of a Next Generation Clustered Heat Map (NGCHM). | ngchmOverview-class |
| Class representing a Generic Property for a Next Generation Clustered Heat Map (NGCHM). | ngchmProperty-class |
| Check Protocol Parameters for NG-CHM | ngchmProtoParamCheck |
| Push a local shaidy repository onto the stack of source repositories | ngchmPushSourceRepository |
| Push a shaidy server onto the stack of source repositories | ngchmPushSourceServer |
| Push Temporary Repository for NG-CHM | ngchmPushTempRepository |
| Register an ngchmServer. | ngchmRegisterServer |
| Class representing a link related to a NGCHM | ngchmRelated-class |
| Class representing a group of related links to a NGCHM | ngchmRelatedGroup-class |
| Render a shaidy NGCHM | ngchmRenderChm |
| Return response content interpreted as JSON | ngchmResponseJSON |
| Row center a shaidy dataset | ngchmRowCenter |
| Save a numeric matrix as a blob in a shaidy repository | ngchmSaveAsDatasetBlob |
| Save a dendrogram as a blob in a shaidy repository | ngchmSaveAsDendrogramBlob |
| Save an NGCHM as a shaidy blob | ngchmSaveChmAsBlob |
| Class representing a Next Generation Clustered Heat Map (NGCHM) server. | ngchmServer-class |
| Class representing a deployment method for a Next Generation Clustered Heat Map (NGCHM) server. | ngchmServerProtocol-class |
| Class representing a Template attached to a NGCHM | ngchmTemplate-class |
| Get the tiles for a shaidy dataset | ngchmTileDataset |
| Class representing a type mapper function for Next Generation Clustered Heat Map (NGCHM). | ngchmTypeMapper-class |
| Unregister NG-CHM Server | ngchmUnregisterServer |
| Class representing the properties of a data point in a Next Generation Clustered Heat Map (NGCHM). | ngchmValueProp-class |
| Class representing ngchmVersion2 object | ngchmVersion2-class |
| Optional Dendrogram | optDendrogram-class |
| Open the NG-CHM on the specified server in the viewer. | plot.ngchmVersion2 |
| Pretty Print NGCHM Type Information | print.ngchm.type.info |
| Print a shaidy repository | print.shaidyRepo |
| Class representing the shaid of an object | shaid-class |
| Add data file(s) and properties to a local shaidy repository | shaidyAddFileBlob |
| Determine if one more blobs exist in a shaidy repository | shaidyBlobExists |
| Copy a blob from one repository to another | shaidyCopyBlob |
| Create a prototype blob in a shaidy repository | shaidyCreateProtoBlob |
| Finalize a prototype blob | shaidyFinalizeProtoBlob |
| Find the first repository, if any, that contains the requested shaid | shaidyFindRepo |
| Get an object's component shaids | shaidyGetComponents shaidyGetComponents,ngchm-method shaidyGetComponents,ngchmCovariate-method shaidyGetComponents,ngchmDataset-method |
| Get shaid for an object | shaidyGetShaid shaidyGetShaid,ngchm-method |
| Compute the shaid to assign a protoblob | shaidyHashProtoBlob |
| Create and initialize Shaidy Repository | shaidyInitRepository |
| Load the provid -> shaid DB for a local shaidy repository | shaidyLoadProvenanceDB |
| Load the provid -> labels DB for a local shaidy repository. | shaidyLoadProvidDB |
| Load a shaidy repository | shaidyLoadRepository |
| Create in memory shaid cache | shaidyNewCache |
| Create a provid from a list of label values | shaidyProvenance |
| Get the methods for the repository API called api | shaidyRepoAPI |
| Helper class for setting row/col gap locations as tree cuts | treeCuts-class |
| Helper function to verify if variable is numeric. | verifyNumeric |
