Department of Bioinformatics and Computational Biology

Navigating Clustered Heatmaps

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Contents

Using the NG-CHM Viewer

We have developed a series of tutorials and videos describing key features of the NG-CHM Viewer:

Topic Video
Quick Tour (ppt) N/A
Display Components and Interactivity Features (video)
Panning and Zooming (video)
Selections (video)
Context-sensitive menus (video)
Color schemes (video)
Covariate Bars (video)

Introduction to Next-Generation (Clustered) Heat Maps

Next-Generation (Clustered) Heat Maps (NG-CHM) are highly interactive, dynamic (clustered) heat maps that enable the user to see an overview of the entire heat map, and via navigation controls, to zoom and pan across the heatmap to see details of the heatmap at many levels of resolution. Other controls enable searching for specific heatmap entries, generating production quality PDFs, and linking out to information related to rows, columns, and individual heatmap entries. The user interface is mostly intuitive, although a few less commonly used features can only be accessed with the use of specific keys.

This page describes how to navigate a NG-CHM using the NG-CHM Viewer. It presumes that you are interacting with a NG-CHM that has already been loaded on a NG-CHM web server. In addition to these pages, we have also produced a video describing the capabilities of the NG-CHM viewer.

Launching the NG-CHM Viewer

The NG-CHM Viewer is a web application.  You can use most web browsers including Firefox, Safari and Chrome. Although many features will work on IE, some will not.  (We are striving to eliminate such issues, but new feature development is our first priority at this time.)  You do not need any special plugins or other browser software installed, but you will need to have Javascript enabled.

If you know the name of the map, you can point a browser directly to it using the following URL format:

http://bioinformatics.mdanderson.org/chm/chm.html?name=YOUR-NGCHM-NAME

You can also see a searchable list of available maps by not specifying a specific NG-CHM name. For instance:

http://bioinformatics.mdanderson.org/chm/

These examples use our NG-CHM server at MD Anderson. If the NG-CHM you wish to access is on a different server, you will need to substitute that server's URL.

Help and Feedback

If you have any comments or questions about the CHM tool, contact Bradley Broom.