Next Generation Clustered Heat Maps

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Documentation for package ‘NGCHM’ version 1.0.4

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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