Man pages for bmbroom/NGCHMR
Utilities for Creating Next Generation Clustered Heat Maps

cash-.shaidyRepoProvide a simpler method for accessing repo methods
chmAddAxisType-methodAdd an axis type to a NGCHM.
chmAddColormap-methodAdd a colormap to a NGCHM.
chmAddCovariateBar-methodAdd a covariate bar to a NGCHM.
chmAddCovariate-methodAdd a covariate to an auxiliary dataset.
chmAddCSS-methodAdd custom CSS to a NGCHM.
chmAddDataset-methodAdd an auxiliary dataset to a NGCHM.
chmAddDialog-methodAdd an extra dialog to a NGCHM.
chmAddLayer-methodAdd a Layer to a NGCHM.
chmAddMenuItem-methodAdd a menu entry to a NGCHM.
chmAddMetaData-methodAdd meta data.
chmAdd-methodAdd a list of objects to a NGCHM.
chmAddOverview-methodGenerate an overview image of the NGCHM when making it.
chmAddProperty-methodAdd custom property to a NGCHM.
chmAddRelatedGroup-methodAdd a group of related links to the NGCHM.
chmAddRelated-methodAdd a link to related information to the NGCHM.
chmAddSpecificAxisTypeFunction-methodAdd a CHM-specific axis type function to a NGCHM.
chmAddTag-methodAdd tags to a NGCHM.
chmAddTemplate-methodAdd a file template to the NGCHM.
chmAddToolboxR2-methodAdd standard toolbox to an element
chmAddToolboxRC-methodAdd standard toolbox to an element
chmAddToolboxR-methodAdd standard toolbox to an axis
chmAxisCreate a new Axis for adding to an NG-CHM.
chmAxisTypeCreate a new AxisType for adding to an ngchmAxis.
chmBindFunction-methodBind values to an existing JS function.
chmBrowseBrowse the NGCHMs on the specified server in the viewer.
chmColOrder-methodSet the column order of data shown in a NGCHM.
chmCreateCollectionCreate a new collection
chmCreateManagedServerCreate an ngchmServer object for a managed NG-CHM server
chmCreateServerCreate an ngchmServer object from a specification.
chmCurrentCollectionGet the user's current collection
chmCurrentServerGet the user's current server
chmDefaultColOrderReturn default column order of an NGCHM
chmDefaultRowOrderReturn default row order of an NGCHM
chmDeployServer-methodGet the name of a NGCHM server.
chmExportToFile-methodExport a standalone NGCHM to a file.
chmExportToPDF-methodExport a PDF of the NGCHM to a file.
chmFieldAccessFunctionGet Javascript function name for accessing a specific string...
chmGetDataset-methodGet the dataset from an NG-CHM object
chmGetDeployServerConfigGet per-user configuration for a specific deploy Server.
chmGetFunctionGet a predefined Javascript function for use in NGCHM menus
chmGetOverviewGet the file path to the specified overview file.
chmGetProperty-methodGet a property value from an NG-CHM object
chmGetTypeInfoGet information about a type name.
chmGetURL-methodGet the URL for an installed NGCHM.
chmHasProperty-methodDetermine if the NG-CHM has the given property.
chmInstall-methodAdd an NG-CHM to an NG-CHM collection.
chmListFunctionsList the predefined Javascript functions available for use in...
chmListServersReturn the names of the NGCHM servers defined to date in this...
chmListTypesList known axis types.
chmLoadCHM-methodLoad CHM from NG-CHM server
chmMake-methodCompile a NGCHM.
chmMakePrivate-methodMake an installed NGCHM private.
chmMakePublic-methodMake an installed NGCHM public.
chmManagerManage the NGCHMs on the specified server in the viewer.
chmName-methodGet the name of a NGCHM.
chmNewCreate a new NGCHM.
chmNewColorMapCreate a new Color Map for use in constructing a NGCHM
chmNewCovariateCreate a new Covariate for adding to an NGCHM auxilary...
chmNewCovariateBarCreate a new covariate Bar for a NGCHM
chmNewDataLayerCreate a new Data Layer for a NGCHM.
chmNewDatasetCreate a new Dataset for a NGCHM.
chmNewDialogCreate a new Dialog for a NGCHM.
chmNewFunctionCreate a new Javascript function for adding to a NGCHM menu.
chmNewPropertyCreate a new Property for adding to a NGCHM.
chmNewServerCreate a new object representing a NGCHM server.
chmOriginalColOrderReturn original column order of an NGCHM
chmOriginalRowOrderReturn original row order of an NGCHM
chmPropertiesCreate a list of NGCHM properties.
chmRandomColOrderReturn random column order of an NGCHM
chmRandomRowOrderReturn random row order of an NGCHM
chmRegisterAxisFunctionRegister a predefined Javascript function for use in NGCHM...
chmRegisterFunctionRegister a predefined Javascript function for use in NGCHM...
chmRegisterGetMetadataFunctionDefine and register a Javascript function for obtaining a...
chmRegisterMatrixFunctionRegister a predefined Javascript function for use in NGCHM...
chmRegisterToolboxFunctionRegister a Javascript function for use in the NGCHM toolbox.
chmRegisterTypeRegister a type name.
chmRegisterTypeMapperRegister a predefined Javascript function for converting...
chmRegisterTypeSplitterDefine and register a Javascript function for converting a...
chmRowOrder-methodSet the row order of data shown in a NGCHM.
chmServerGet a registered ngchmServer object for use in making and...
chmSetCollectionSet the user's current server and/or collection
chmSetCredentials-methodSet access credentials.
chmSetDeployServerConfigSpecify per-user configuration for a specific deploy Server.
chmStringopFunctionGet Javascript function name for performing a specific string...
chmUninstall-methodRemove an installed NGCHM.
chmUrlBase-methodGet the base URL for a NGCHM installed on a NGCHM server.
chmUserDendrogramToShaidConvert a user specified dendrogram to a shaid
chmUserLabelsToShaidConvert user specified labels to a shaid
chmWriteCustomJSOutput Javascript code required to customize an NGCHM.
cos.dist1Compute cosine (angular) distance matrix
gitHashObjectObtain the git hash of an existing file.
ngchmAddDatasetBlobAdd a data file to a local shaidy repository
ngchmAddMatrixToCollectionAdd a matrix reference to a collection
ngchmAddObjectToCollectionAdd an object reference to a collection
ngchmAxis-classClass representing an axis of a Next Generation Clustered...
ngchmAxisFunction-classClass representing an axis function for Next Generation...
ngchmAxisType-classClass representing a type attached to an axis in a Next...
ngchmBar-classClass representing a Covariate Bar on a Next Generation...
ngchm-classClass representing a Next Generation Clustered Heat Map...
ngchmCollectionInCollectionRecursively determine if collection uuid is contained in...
ngchmCollectionTreeCreate a recursive description of a collection
ngchmColormap-classClass representing a Color Map on a Next Generation Clustered...
ngchmCovariate-classClass representing a Covariate attached to a Dataset
ngchmCreateServerProtocolCreate and register an NGCHM server protocol implementation.
ngchmCSS-classClass representing custom CSS for a Next Generation Clustered...
ngchmDataset-classClass representing a Dataset attached to a NGCHM
ngchmDialog-classClass representing an addon dialog
ngchmFindRepoFind a repository, if any, that contains the requested shaid
NGCHM-functionsJavascript extensions for the Next Generation Clustered Heat...
ngchmGetDataFileShaidCompute shaid for a data file
ngchmGetEnvGet the ngchm environment (for debugging only).
ngchmGetHandleHTTRGet a HTTR handle for the server's view/WS URL
ngchmGetLabelsGet the axis labels of a shaidy dataset or dendrogram
ngchmGetLabelsStrGet the axis labels of a shaidy dataset or dendrogram
ngchmGetProtoParamGet a server protocol parameter
ngchmGetServerProtocolLookup a Server Protocol
NGCHM-initializationInitialization of the NGCHM library.
ngchmInitShaidyRepositoryCreate a shaidy repository for NG-CHMS
ngchmJS-classClass representing a custom Javascript function for a Next...
ngchmLayer-classClass representing a Layer on a Next Generation Clustered...
ngchmListServerProtocolsList defined server protocols
ngchmLoadDatasetBlobLoad a data matrix from a local shaidy repository
ngchmMakeFormat.originalMake an original format NGCHM.
ngchmMakeFormat.shaidyMake a shaidy format NGCHM.
ngchmMatrixFunction-classClass representing a matrix function for Next Generation...
ngchmMenuItem-classClass representing a Menu Item for a Next Generation...
ngchmMetaData-classClass representing meta data attached to an NG-CHM
ngchmNewBarCreate a new Classification Bar for a NGCHM
ngchmNewCollectionCreate a new collection in a local shaidy repository
ngchmOverview-classClass representing an overview of a Next Generation Clustered...
NGCHM-packageNext Generation Clustered Heat Map (NGCHM) Construction...
ngchmProperty-classClass representing a Generic Property for a Next Generation...
ngchmProtoParamCheckCheck that all required parameters are specified, and all...
ngchmPushSourceRepositoryPush a shaidy repository onto the stack of source...
ngchmPushTempRepositoryPush a shaidy repository onto the stack of temporary...
ngchmRegisterServerRegister an ngchmServer.
ngchmRelated-classClass representing a link related to a NGCHM
ngchmRelatedGroup-classClass representing a group of related links to a NGCHM
ngchmRenderChmRender a shaidy NGCHM
ngchmResponseJSONReturn response content interpreted as JSON
ngchmRowCenterRow center a shaidy dataset
ngchmSaveAsDatasetBlobSave a numeric matrix as a blob in a shaidy repository
ngchmSaveAsDendrogramBlobSave a dendrogram as a blob in a shaidy repository
ngchmSaveChmAsBlobSave an NGCHM as a shaidy blob
ngchmServer-classClass representing a Next Generation Clustered Heat Map...
ngchmServerProtocol-classClass representing a deployment method for a Next Generation...
ngchmShaidyInitInitialize shaidy subsystem for NGCHMs
ngchmTemplate-classClass representing a Template attached to a NGCHM
ngchmTileDatasetGet the tiles for a shaidy dataset
ngchmTypeMapper-classClass representing a type mapper function for Next Generation...
ngchmUnregisterServerUnregister ngchmServer(s).
ngchmValueProp-classClass representing the properties of a data point in a Next...
optDendrogram-classOptional Dendrogram
plot.ngchmVersion2Open the NG-CHM on the specified server in the viewer.
print.ngchm.type.infoPretty print the result returned by chmGetTypeInfo.
print.shaidyRepoPrint a shaidy repository
readTileRead a binary viewer tile as a matrix
shaid-classClass representing the shaid of an object
shaidyAddFileBlobAdd data file(s) and properties to a local shaidy repository
shaidyBlobExistsDetermine if one more blobs exist in a shaidy repository
shaidyCopyBlobCopy a blob from one repository to another
shaidyCreateProtoBlobCreate a prototype blob in a shaidy repository
shaidyFinalizeProtoBlobFinalize a prototype blob
shaidyFindRepoFind the first repository, if any, that contains the...
shaidyGetComponents-methodGet an object's component shaids
shaidyGetShaid-methodGet shaid for an object
shaidyHashProtoBlobCompute the shaid to assign a protoblob
shaidyInitInitialize the shaidy subsystem
shaidyInitRepositoryCreate and initialize a local shaidy repository.
shaidyLoadProvenanceDBLoad the provid -> shaid DB for a local shaidy repository
shaidyLoadProvidDBLoad the provid -> labels DB for a local shaidy repository.
shaidyLoadRepositoryLoad a shaidy repository
shaidyNewCacheCreate in memory shaid cache
shaidyProvenanceCreate a provid from a list of label values
shaidyRegisterRepoAPISet the methods for the repository API called api
shaidyRepoAPIGet the methods for the repository API called api
TCGA.GBM.EXPRSample dataset containing RNA expression data from Affymetrix...
validateNewLayerCheck that the specified layer can be added to the specificed...
writeTileWrite a matrix as a binary viewer tile
bmbroom/NGCHMR documentation built on July 28, 2018, 11:17 a.m.