Department of Bioinformatics and Computational Biology

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Display Components and Interactivity Features

The window is divided into several major display and interaction areas as detailed below. Specific features mentioned in the text are identified by numbered yellow circles superimposed on the screen shot images.

Main Viewing Area

This area includes the central heat map display (1) as well as optional dendrograms (2), classifications (3), and labels (10).

Central Heat Map Display (1)

Navigation operations: The following operations are available when the cursor is on the central heat map display (1):

As you move around, the dendrograms, classifications, and labels will also move around to stay in sync with the central heat map display.

Other operations:

Dendrograms (2)

Dendrograms, if present, will appear on the top or left. Right click (Control-click on a Mac) on the main data area to bring up the matrix menu. The menu will be based on the selected branches. Click a branch to select a branch. Shift-click on a branch to add or remove it from the current selections. The detailed elements of the dendrogram may be replaced by a solid bar if they are too small to be displayed. This bar may be shown in an alternate color to indicate that the dendrogram was trimmed at that point. As you zoom in, the dendrogram will increase in size and additional details will be included.

Classification Bars (3)

Classification bars, if present, will appear between the dendrogram (if present) and the central heat map display.

Axis Labels (10)

Axis labels are displayed once the image has been zoomed in enough for them to be legible. Right-click (Control-click on a Mac) on the label area to bring up the label menu. The menu will be based on the selected labels. Click a label to select a label. Shift-click to add or remove a label from the current selections. You can also shift and drag over the labels to select them, even if the map is not zoomed in enough to display the labels. The options available in the menu are specified when the NG-CHM is constructed.

Dialog Windows

Detailed information about the NG-CHM and additional interactive controls are contained in a variety of dialog boxes that can be displayed if the user desires. When an NG-CHM is first opened, several dialog boxes may be displayed depending on options selected when the NG-CHM was created. Additional dialog boxes can be displayed by pressing the appropriate button in the menu bar (see below). Dialog boxes can be positioned anywhere within the current browser window by dragging the dialog box title bar. Dialog boxes can be closed by clicking on the cross displayed in the dialog box title bar. Closed dialog boxes can be reopened.

Help Dialog

Contains a very brief summary of the main NG-CHM navigation controls, and key links to additional user documentation.

Navigator Dialog (9)

The navigator dialog shows a high-level view of the entire NG-CHM. A rectangular selection in the navigator window shows the portion of the entire NG-CHM that is shown in the central heat map display.

Navigation operations:

Color Scheme Dialog (8)

This is the key for the current color scheme. The key also displays which image is visible, and which color schemes are used by each. The panel also includes to select new color schemes. Existing color schemes can be selected by clicking on the text link on the left. New color schemes can be chosen by selecting the desired ceiling, middle, floor and missing colors and then pressing the Render button. If a CHM has multiple data sets, whichever view is currently visible is the one that will be recolored. The floor value should be less than the middle value, which should be less than the ceiling value. New color schemes are available for the remainder of your browser session.

Advanced Search Dialog (11)

This dialog searches the map based on the row and column labels. The axes can be searched together or separately. Use the search results to jump to the corresponding portion of the map.

Image Details Dialog (6)

As the main image is moused over the underlying information for the current data point is displayed in this dialog, as are the corresponding row and column labels.

Classification Details Dialog (7)

Displays color key for the current classification bar.

Credits Dialog

Displays information about the developers and financial supporters behind NG-CHM.

Top Bar and Menu Area

The top bar (5) displays commonly used information and interactive controls. Some of the features will only be active if particular information was included when the NG-CHM was created.

Layer Names (4)

When a NG-CHM is created, at least one and perhaps several data layers may be associated with it. At any time, the central heat map display can show any one of these layers. The name of currently displayed data layer is shown in this part of the top bar. If the NG-CHM contains more than one data layer, the name of the alternate layer is also displayed. The “Main’ and ‘Flick’ links will switch to the corresponding layer, and the arrow beside those links both indicates the current selection and swaps the current and alternate data layers. If a map was created with more than two layers, you can choose any of them to be the ‘Main’ or the ‘Flick’ layer.


The Arrows on the Top Bar undo and redo recent operations. Click to operate on the most recent step. Right-click (Control-click on a Mac) to jump to a different point in the log.


The home icon will take users to the CHM home page.




Search Box

A search term can be entered in the field labeled ‘Search Term’. The search term will match any label that has a partial match to the search term, but additional wild cards can be used as well.