Function reference • NGCHMR

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

Reference

Creating and Saving a NG-CHM

Covariate Bars

Color Maps and Data Layers

Specifying Axis Type

Alphabetical List