R: Next Generation Clustered Heat Maps

# Next Generation Clustered Heat Maps

## Documentation for package ‘NGCHM’ version 1.0.3

- DESCRIPTION file.

## Help Pages

C G I N O P S T V misc

NGCHM-package | Next Generation Clustered Heat Map (NGCHM) Construction Library

## -- C --

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.
chmAdd-method | Add a list of objects to a NGCHM.
chmAddAxisType | Add an axis type to a NGCHM.
chmAddAxisType-method | Add an axis type to a NGCHM.
chmAddColormap | Add a colormap to a NGCHM.
chmAddColormap-method | Add a colormap to a NGCHM.
chmAddCovariate | Add a covariate to an auxiliary dataset.
chmAddCovariate-method | Add a covariate to an auxiliary dataset.
chmAddCovariateBar | Add a covariate bar to a NGCHM.
chmAddCovariateBar-method | Add a covariate bar to a NGCHM.
chmAddCSS | Add custom CSS to a NGCHM.
chmAddCSS-method | Add custom CSS to a NGCHM.
chmAddDataset | Add an auxiliary dataset to a NGCHM.
chmAddDataset-method | Add an auxiliary dataset to a NGCHM.
chmAddDialog | Add an extra dialog to a NGCHM.
chmAddDialog-method | Add an extra dialog to a NGCHM.
chmAddLayer | Add a Layer to a NGCHM.
chmAddLayer-method | Add a Layer to a NGCHM.
chmAddMenuItem | Add a menu entry to a NGCHM.
chmAddMenuItem-method | Add a menu entry to a NGCHM.
chmAddMetaData | Add MetaData to NG-CHM
chmAddMetaData-method | Add MetaData to NG-CHM
chmAddOverview | Generate an overview image of the NGCHM when making it.
chmAddOverview-method | 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.
chmAddProperty-method | 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.
chmAddRelated-method | Add a link to related information to the NGCHM.
chmAddRelatedGroup | Add a group of related links to the NGCHM.
chmAddRelatedGroup-method | Add a group of related links to the NGCHM.
chmAddSpecificAxisTypeFunction | Add a CHM-specific axis type function to a NGCHM.
chmAddSpecificAxisTypeFunction-method | Add a CHM-specific axis type function to a NGCHM.
chmAddTag | Add tags to a NGCHM.
chmAddTag-method | Add tags to a NGCHM.
chmAddTemplate | Add a file template to the NGCHM.
chmAddTemplate-method | Add a file template to the NGCHM.
chmAddToolboxR | Add standard toolbox to an NG-CHM axis
chmAddToolboxR-method | Add standard toolbox to an NG-CHM axis
chmAddToolboxR2 | Add Toolbox R2 to NG-CHM
chmAddToolboxR2-method | Add Toolbox R2 to NG-CHM
chmAddToolboxRC | Add Toolbox RC to NG-CHM
chmAddToolboxRC-method | Add Toolbox RC to NG-CHM
chmAddTSNE | Add TSNE coordinates to an 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.
chmBindFunction-method | 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.
chmColOrder<--method | Set the column order of data shown in a NGCHM.
chmColorMap | Get the color map of an NG-CHM object.
chmColorMap<- | Set the color map of an NG-CHM object
chmColors | Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCovariate.
chmColors<- | Set 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.
chmDeployServer-method | 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
chmGetDataset-method | 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
chmGetProperty-method | Get Property from NG-CHM
chmGetTypeInfo | Get information about a type name.
chmGetURL | Get the URL for an installed NGCHM.
chmGetURL-method | Get the URL for an installed NGCHM.
chmHasProperty | Determine if the NG-CHM has the given property.
chmHasProperty-method | Determine if the NG-CHM has the given property.
chmInstall | Add an NG-CHM to an NG-CHM collection.
chmInstall-method | Add an NG-CHM to an NG-CHM collection.
chmLabel | Get the label/name of an NG-CHM object.
chmLabel<- | Set the label/name of an NG-CHM object
chmLayer | Get a specified Data Layer from an NG-CHM.
chmLayer<- | Set (or append) a specified Data Layer in 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
chmLoadCHM-method | Load CHM from NG-CHM server
chmLoadShaidyCHM | Load an NG-CHM from an NG-CHM server.
chmMake | Compile a NGCHM.
chmMake-method | Compile a NGCHM.
chmMakePrivate | Make NG-CHM Private on Server
chmMakePrivate-method | Make NG-CHM Private on Server
chmMakePublic | Make NG-CHM Public on Server
chmMakePublic-method | Make NG-CHM Public on Server
chmManager | Open the NG-CHM Manager
chmName | Get the name of a NGCHM.
chmName-method | 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 | Get the value of an NG-CHM property.
chmProperty<- | Set 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.
chmRowOrder<--method | 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
chmSetCredentials-method | 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
chmUninstall-method | Remove an NG-CHM from Server
chmUrlBase | Get the base URL for a NGCHM installed on a NGCHM server.
chmUrlBase-method | Get the base URL for a NGCHM installed on a NGCHM server.
chmWriteCustomJS | Output Javascript code required to customize an NGCHM.

## -- G --

getDimensions | Generic method to get a dimensions matrix from obj.
getDimensions,prcomp | Generic method to get a dimensions matrix from obj.
getDimensions,Seurat | Generic method to get a dimensions matrix from obj.
getDimensions,umap | Generic method to get a dimensions matrix from obj.
getDimensions.default | Generic method to get a dimensions matrix from obj.
getDimensions.prcomp | Generic method to get a dimensions matrix from obj.
getDimensions.Seurat | Generic method to get a dimensions matrix from obj.
getDimensions.umap | Generic method to get a dimensions matrix from obj.
gitHashObject | Obtain the git hash of an existing file.

## -- I --

initLogging | Initialize Logging

## -- N --

NGCHM | Next Generation Clustered Heat Map (NGCHM) Construction Library
ngchm-class | Class representing a Next Generation Clustered Heat Map (NGCHM) under construction.
NGCHM-functions | Javascript extensions for the Next Generation Clustered Heat Map (NGCHM) Construction Library
NGCHM-initialization | Initialization of the NGCHM library.
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).
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.
ngchmCSS-class | Class representing custom CSS for a Next Generation Clustered Heat Map (NGCHM).
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

## -- O --

optDendrogram-class | Optional Dendrogram

## -- P --

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

## -- S --

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
shaidyGetComponents-method | Get an object's component shaids
shaidyGetShaid | Get shaid for an object
shaidyGetShaid-method | 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

## -- T --

treeCuts-class | Helper class for setting row/col gap locations as tree cuts

## -- V --

verifyNumeric | Helper function to verify if variable is numeric.

## -- misc --

$.shaidyRepo | Provide a simpler method for accessing repo methods
+ | Add an Axis to an NG-CHM Version 2
+-method | Add an Axis to an NG-CHM Version 2