Next Generation Clustered Heat Maps
Add an Axis to an NG-CHM Version 2
Provide a simpler method for accessing repo methods
Helper function to cast variables as integers.
Helper function to cast list as integer
Add a list of objects to a NGCHM.
Add an axis type to a NGCHM.
Add a colormap to a NGCHM.
Add a covariate to an auxiliary dataset.
Add a covariate bar to a NGCHM.
Add custom CSS to a NGCHM.
Add an auxiliary dataset to a NGCHM.
Add an extra dialog to a NGCHM.
Add a Layer to a NGCHM.
Add a menu entry to a NGCHM.
Add MetaData to NG-CHM
Generate an overview image of the NGCHM when making it.
Add PCA coordinates to an NG-CHM.
Add custom property to a NGCHM.
Add reduced dimension coordinates to an NG-CHM.
Add a link to related information to the NGCHM.
Add a group of related links to the NGCHM.
Add a CHM-specific axis type function to a NGCHM.
Add tags to a NGCHM.
Add a file template to the NGCHM.
Add standard toolbox to an NG-CHM axis
Add Toolbox R2 to NG-CHM
Add Toolbox RC to NG-CHM
Add TSNE coordinates to an NG-CHM.
Add UMAP coordinates to an NG-CHM.
Add UWOT::UMAP coordinates to an NG-CHM.
Create a new Axis for adding to an NG-CHM.
Create a new AxisType for adding to an ngchmAxis.
Bind values to an existing JS function.
Browse the NGCHMs on the specified server in the viewer.
Set the column order of data shown in a NGCHM.
Set the color map of an NG-CHM object
Get the color map of an NG-CHM object.
Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCova...
Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or ngchmCova...
Get a covariate attached to an NG-CHM dataset.
Get a covariate bar attached to an NG-CHM.
Create a new NG-CHM Collection
Create an ngchmServer object for a managed NG-CHM server
Create an ngchmServer object from a specification.
Get the user's current collection
Get the user's current server
Return default column order of an NGCHM
Return default row order of an NGCHM
Get the name of a NGCHM server.
Export a standalone NGCHM to a file.
Export a standalone HTML containing the NGCHM to a file.
Export a PDF of the NGCHM to a file.
Get Javascript function name for accessing a specific string field in ...
Get the dataset from an NG-CHM object
Get per-user configuration for a specific deploy Server.
Get a predefined Javascript function for use in NGCHM menus
Get the file path to the specified overview file.
Get Property from NG-CHM
Get information about a type name.
Get the URL for an installed NGCHM.
Determine if the NG-CHM has the given property.
Add an NG-CHM to an NG-CHM collection.
Set the label/name of an NG-CHM object
Get the label/name of an NG-CHM object.
Set (or append) a specified Data Layer in an NG-CHM.
Get a specified Data Layer from an NG-CHM.
List the predefined Javascript functions available for use in NGCHM me...
List NG-CHM Servers
List known axis types.
Load CHM from NG-CHM server
Load an NG-CHM from an NG-CHM server.
Compile a NGCHM.
Make NG-CHM Private on Server
Make NG-CHM Public on Server
Open the NG-CHM Manager
Get the name of a NGCHM.
Create a new NGCHM.
Create a new Color Map for use in constructing a NGCHM
Create a new Covariate for adding to an NGCHM auxilary dataset.
Create a new covariate Bar for a NGCHM
Create a new Data Layer for a NGCHM.
Create a new Dataset for a NGCHM.
Create a new Dialog for a NGCHM.
Create a new Javascript function for adding to a NGCHM menu.
Create a new Property for adding to a NGCHM.
Create a new object representing a NGCHM server.
Return original column order of an NGCHM
Return original row order of an NGCHM
Create NG-CHM Properties
Set the value of an NG-CHM property.
Get the value of an NG-CHM property.
Return random column order of an NGCHM
Return random row order of an NGCHM
Register a predefined Javascript function for use in NGCHM Axis menus.
Register a predefined Javascript function for use in NGCHM menus.
Define and register a Javascript function for obtaining a specific met...
Register a predefined Javascript function for use in NGCHM Matrix menu...
Register a Javascript function for use in the NGCHM toolbox.
Register a type name.
Register a predefined Javascript function for converting values from o...
Define and register a Javascript function for converting a lists of ty...
Set the row order of data shown in a NGCHM.
Get a registered ngchmServer object for use in making and installing N...
Set the user's current server and/or collection
Set Access Credentials for NG-CHM Server
Specify per-user configuration for a specific deploy Server.
Get Javascript function name for performing a specific string operatio...
Creates new treeCuts object
Remove an NG-CHM from Server
Get the base URL for a NGCHM installed on a NGCHM server.
Output Javascript code required to customize an NGCHM.
Generic method to get a dimensions matrix from obj.
Obtain the git hash of an existing file.
Initialize Logging
Class representing a Next Generation Clustered Heat Map (NGCHM) under ...
Javascript extensions for the Next Generation Clustered Heat Map (NGCH...
Initialization of the NGCHM library.
Next Generation Clustered Heat Map (NGCHM) Construction Library
Add a data file to a local shaidy repository
Add a matrix reference to a collection
Add an object reference to a collection
Class representing an axis of a Next Generation Clustered Heat Map (NG...
Class representing an axis function for Next Generation Clustered Heat...
Class representing a type attached to an axis in a Next Generation Clu...
Class representing a Covariate Bar on a Next Generation Clustered Heat...
Recursively determine if collection uuid is contained in collection A ...
Create a recursive description of a collection
Class representing a Color Map on a Next Generation Clustered Heat Map...
Class representing a Covariate attached to a Dataset
Create and register an NGCHM server protocol implementation.
Class representing custom CSS for a Next Generation Clustered Heat Map...
Class representing a Dataset attached to a NGCHM
Class representing an addon dialog
Find a repository, if any, that contains the requested shaid
Compute shaid for a data file
Get the ngchm environment (for debugging only).
Get a HTTR handle for the server's view/WS URL
Get the axis labels of a shaidy dataset or dendrogram
Get the axis labels of a shaidy dataset or dendrogram
Get Protocol Parameter for NG-CHM Server
Get Server Protocol for NG-CHM
Initialize Shaidy Repository for NG-CHM
Class representing a custom Javascript function for a Next Generation ...
Class representing a Layer on a Next Generation Clustered Heat Map (NG...
List defined server protocols
Load a data matrix from a local shaidy repository
Make an original format NGCHM.
Make a shaidy format NGCHM.
Class representing a matrix function for Next Generation Clustered Hea...
Class representing a Menu Item for a Next Generation Clustered Heat Ma...
Class representing meta data attached to an NG-CHM
Create a new Classification Bar for a NGCHM
Create a new collection in a local shaidy repository
Class representing an overview of a Next Generation Clustered Heat Map...
Class representing a Generic Property for a Next Generation Clustered ...
Check Protocol Parameters for NG-CHM
Push a local shaidy repository onto the stack of source repositories
Push a shaidy server onto the stack of source repositories
Push Temporary Repository for NG-CHM
Register an ngchmServer.
Class representing a link related to a NGCHM
Class representing a group of related links to a NGCHM
Render a shaidy NGCHM
Return response content interpreted as JSON
Row center a shaidy dataset
Save a numeric matrix as a blob in a shaidy repository
Save a dendrogram as a blob in a shaidy repository
Save an NGCHM as a shaidy blob
Class representing a Next Generation Clustered Heat Map (NGCHM) server...
Class representing a deployment method for a Next Generation Clustered...
Class representing a Template attached to a NGCHM
Get the tiles for a shaidy dataset
Class representing a type mapper function for Next Generation Clustere...
Unregister NG-CHM Server
Class representing the properties of a data point in a Next Generation...
Class representing ngchmVersion2 object
Optional Dendrogram
Open the NG-CHM on the specified server in the viewer.
Pretty Print NGCHM Type Information
Print a shaidy repository
Class representing the shaid of an object
Add data file(s) and properties to a local shaidy repository
Determine if one more blobs exist in a shaidy repository
Copy a blob from one repository to another
Create a prototype blob in a shaidy repository
Finalize a prototype blob
Find the first repository, if any, that contains the requested shaid
Get an object's component shaids
Get shaid for an object
Compute the shaid to assign a protoblob
Create and initialize Shaidy Repository
Load the provid -> shaid DB for a local shaidy repository
Load the provid -> labels DB for a local shaidy repository.
Load a shaidy repository
Create in memory shaid cache
Create a provid from a list of label values
Get the methods for the repository API called api
Helper class for setting row/col gap locations as tree cuts
Helper function to verify if variable is numeric.
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.
Useful links