Package: NGCHM 1.0.3

Mary A Rohrdanz

NGCHM: Next Generation Clustered Heat Maps

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.

Authors:Bradley M Broom [aut], Mary A Rohrdanz [ctb, cre], Chris Wakefield [ctb], James Melott [ctb], MD Anderson Cancer Center [cph]

NGCHM.pdf |NGCHM.html
NGCHM/json (API)

# Install NGCHM in R:
install.packages('NGCHM', repos = c('', ''))

Peer review:

Bug tracker:



147 exports 7 stars 1.94 score 15 dependencies 683 downloads

Last updated 1 months agofrom:e1a26191c496073d7a51e35d89485f270238819c



Readme and manuals

Help Manual

Help pageTopics
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 integercastListAsInteger
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-CHMchmAddMetaData 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 axischmAddToolboxR chmAddToolboxR,ngchm,character,character,character,character-method
Add Toolbox R2 to NG-CHMchmAddToolboxR2 chmAddToolboxR2,ngchm,character,character,character-method
Add Toolbox RC to NG-CHMchmAddToolboxRC 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 objectchmColorMap<-
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 CollectionchmCreateCollection
Create an ngchmServer object for a managed NG-CHM serverchmCreateManagedServer
Create an ngchmServer object from a specification.chmCreateServer
Get the user's current collectionchmCurrentCollection
Get the user's current serverchmCurrentServer
Return default column order of an NGCHMchmDefaultColOrder
Return default row order of an NGCHMchmDefaultRowOrder
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 objectchmGetDataset chmGetDataset,ngchmLayer-method
Get per-user configuration for a specific deploy Server.chmGetDeployServerConfig
Get a predefined Javascript function for use in NGCHM menuschmGetFunction
Get the file path to the specified overview file.chmGetOverview
Get Property from NG-CHMchmGetProperty 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 objectchmLabel<-
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 ServerschmListServers
List known axis types.chmListTypes
Load CHM from NG-CHM serverchmLoadCHM 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 ServerchmMakePrivate chmMakePrivate,character,character-method chmMakePrivate,character,ngchm-method chmMakePrivate,ngchmServer,character-method chmMakePrivate,ngchmServer,ngchm-method
Make NG-CHM Public on ServerchmMakePublic chmMakePublic,character,character-method chmMakePublic,character,ngchm-method chmMakePublic,ngchmServer,character-method chmMakePublic,ngchmServer,ngchm-method
Open the NG-CHM ManagerchmManager
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 NGCHMchmNewColorMap
Create a new Covariate for adding to an NGCHM auxilary dataset.chmNewCovariate
Create a new covariate Bar for a NGCHMchmNewCovariateBar
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 NGCHMchmOriginalColOrder
Return original row order of an NGCHMchmOriginalRowOrder
Create NG-CHM PropertieschmProperties
Get the value of an NG-CHM property.chmProperty
Set the value of an NG-CHM property.chmProperty<-
Return random column order of an NGCHMchmRandomColOrder
Return random row order of an NGCHMchmRandomRowOrder
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 NGCHMschmServer
Set the user's current server and/or collectionchmSetCollection
Set Access Credentials for NG-CHM ServerchmSetCredentials 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 objectchmTreeGaps
Remove an NG-CHM from ServerchmUninstall 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 LogginginitLogging
Next Generation Clustered Heat Map (NGCHM) Construction LibraryNGCHM-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 LibraryNGCHM-functions
Initialization of the NGCHM library.NGCHM-initialization
Add a data file to a local shaidy repositoryngchmAddDatasetBlob
Add a matrix reference to a collectionngchmAddMatrixToCollection
Add an object reference to a collectionngchmAddObjectToCollection
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 collectionngchmCollectionTree
Class representing a Color Map on a Next Generation Clustered Heat Map (NGCHM).ngchmColormap-class
Class representing a Covariate attached to a DatasetngchmCovariate-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 NGCHMngchmDataset-class
Class representing an addon dialogngchmDialog-class
Find a repository, if any, that contains the requested shaidngchmFindRepo
Compute shaid for a data filengchmGetDataFileShaid
Get the ngchm environment (for debugging only).ngchmGetEnv
Get a HTTR handle for the server's view/WS URLngchmGetHandleHTTR
Get the axis labels of a shaidy dataset or dendrogramngchmGetLabels
Get the axis labels of a shaidy dataset or dendrogramngchmGetLabelsStr
Get Protocol Parameter for NG-CHM ServerngchmGetProtoParam
Get Server Protocol for NG-CHMngchmGetServerProtocol
Initialize Shaidy Repository for NG-CHMngchmInitShaidyRepository
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 protocolsngchmListServerProtocols
Load a data matrix from a local shaidy repositoryngchmLoadDatasetBlob
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-CHMngchmMetaData-class
Create a new Classification Bar for a NGCHMngchmNewBar
Create a new collection in a local shaidy repositoryngchmNewCollection
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-CHMngchmProtoParamCheck
Push a local shaidy repository onto the stack of source repositoriesngchmPushSourceRepository
Push a shaidy server onto the stack of source repositoriesngchmPushSourceServer
Push Temporary Repository for NG-CHMngchmPushTempRepository
Register an ngchmServer.ngchmRegisterServer
Class representing a link related to a NGCHMngchmRelated-class
Class representing a group of related links to a NGCHMngchmRelatedGroup-class
Render a shaidy NGCHMngchmRenderChm
Return response content interpreted as JSONngchmResponseJSON
Row center a shaidy datasetngchmRowCenter
Save a numeric matrix as a blob in a shaidy repositoryngchmSaveAsDatasetBlob
Save a dendrogram as a blob in a shaidy repositoryngchmSaveAsDendrogramBlob
Save an NGCHM as a shaidy blobngchmSaveChmAsBlob
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 NGCHMngchmTemplate-class
Get the tiles for a shaidy datasetngchmTileDataset
Class representing a type mapper function for Next Generation Clustered Heat Map (NGCHM).ngchmTypeMapper-class
Unregister NG-CHM ServerngchmUnregisterServer
Class representing the properties of a data point in a Next Generation Clustered Heat Map (NGCHM).ngchmValueProp-class
Class representing ngchmVersion2 objectngchmVersion2-class
Optional DendrogramoptDendrogram-class
Open the NG-CHM on the specified server in the viewer.plot.ngchmVersion2
Pretty Print NGCHM Type
Print a shaidy repositoryprint.shaidyRepo
Class representing the shaid of an objectshaid-class
Add data file(s) and properties to a local shaidy repositoryshaidyAddFileBlob
Determine if one more blobs exist in a shaidy repositoryshaidyBlobExists
Copy a blob from one repository to anothershaidyCopyBlob
Create a prototype blob in a shaidy repositoryshaidyCreateProtoBlob
Finalize a prototype blobshaidyFinalizeProtoBlob
Find the first repository, if any, that contains the requested shaidshaidyFindRepo
Get an object's component shaidsshaidyGetComponents shaidyGetComponents,ngchm-method shaidyGetComponents,ngchmCovariate-method shaidyGetComponents,ngchmDataset-method
Get shaid for an objectshaidyGetShaid shaidyGetShaid,ngchm-method
Compute the shaid to assign a protoblobshaidyHashProtoBlob
Create and initialize Shaidy RepositoryshaidyInitRepository
Load the provid -> shaid DB for a local shaidy repositoryshaidyLoadProvenanceDB
Load the provid -> labels DB for a local shaidy repository.shaidyLoadProvidDB
Load a shaidy repositoryshaidyLoadRepository
Create in memory shaid cacheshaidyNewCache
Create a provid from a list of label valuesshaidyProvenance
Get the methods for the repository API called apishaidyRepoAPI
Helper class for setting row/col gap locations as tree cutstreeCuts-class
Helper function to verify if variable is numeric.verifyNumeric