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Detail and Summary Panels

In addition to the header area described in the Interface Overview tab, an NG-CHM will typically consist of at least two panels, a summary panel and a detail panel. These panels are divided into several major display and interaction areas as detailed below.

The Summary panel (right panel) displays a summarized view of all the data of a layer in the NG-CHM and can be used to select which data is displayed in Detail Matrix panels (left).

Both of these panels display a main matrix and optionally covariates and dendrograms for both rows and columns. In addition a detail panel will display row and column labels for both the main matrix and for covariates if space is available at the current zoom level.

Summary Panel

The summary panel always displays all of the matrix data in the selected layer of the NG-CHM. If this data matrix consists of more rows or columns than there are pixels available to display it, then the data will be summarized using one of a few options and therefore might display colors different from those defined in the map dependent on the summarization method and colors the builder of the map selected when they created the map.

In addition to providing this summarized view of the current layer this panel has other functionality:

• Indicates what rows/columns/areas are selected on the NG-CHM.
• Displays boxes around the areas that are displayed in all detail panels to indicate what parts of the map are being displayed in those detail panels.
• Displays top items defined for the NG-CHM, if any are defined.

• Allows modification of the selection of data to be displayed in the current primary detail pane through several methods to be described below.

  • Clicking on the main matrix area to move the current detail panel to a new part of the matrix.
  • Clicking and dragging on the main matrix area to move the current detail panel to a new part of the matrix.
  • Drag-and-Drop selection on the main matrix area of the summary pane to select a non-proportional detail matrix area.
  • Clicking on the row and/or column dendrogram areas in the summary pane to select or deselect areas.
  • Increasing or descreasing the size of the box displayed in the current detail panel using the mouse wheel.

Navigation operations: The following operations are available when the cursor is on the summary panel area:

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:

• Matrix Menu:
  • Right click (Control-click on a Mac) on the main data area to bring up the matrix menu. This menu will include operations based on the selected rows and columns or the current row and column of the matrix if none were selected.
  • Shift Drag over the main matrix area to select rows and columns. Rows and columns can also be selected through the corresponding dendrograms and labels. The options available in the menu are determined when the CHM was constructed.

Dendrograms

Dendrograms, if present, will appear on the top or left. 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. Selecting a dedrogram region on the summary panel will set the primary detail panel view into horizontal or vertical ribbon mode dependent on the axis selected. See the Detail Panel description below for more details.

Covariate Bars

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

Axis Labels

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.

Top Items

If top items for rows or columns have been defined for the NG-CHM, then they will appear below or to the right of the main matrix respectively.

Making selections in the Summary Panel

Selection operations performed on the Summary Panel will not select rows and columns on the detail view, but will instead select the view shown in the Detail Panel. The Detail Panel will select the closest matching zoom level for the region you wish to view.

Selections on this panel can be made in mutiple ways.

– Clicking on the main matrix area. – Use shift and hold down the left mouse button while dragging the mouse pointer across the main matrix area. – Clicking or shift-clicking on a dendrogram.

For clustered heat maps, a selection option in the Summary Panel can be used to view a section of the map associated with a dendrogram branch. This feature is particularly useful for investigation of sub-sections of the heat map related class of samples (e.g. subgroup of cancer patients identified by a dendrogram branch). Selecting a dendrogram branch in the Summary Panel will lock the Detail Panel to only portion of the heat map associated with the selected branch of the dendrogram. The selected portion of the map is visible as it normally is in the Summary Panel but the non-selected part of the heat map is grayed out. You can scroll up/down or left/right through dendrogram branch data in the Detail Panel. This view is essentially a restricted ribbon view. To get out of the sub-dendrogram view, click on the normal mode button in the primary detail panel.

Detail Panel

Detail Panels are where the most detailed view of the data is available and where many of the user interactions with data in the NG-CHM will occur. A detail panel will display some subset of the data in the matrix.

Like the summary panel, if the visible detail matrix consists of more rows or columns than there are pixels available to display it, then the data will be summarized using one of a few options and therefore might display colors different from those defined in the map dependent on the summarization method and colors the builder of the map selected when they created the map.

Detail Panel Header

The header area for a detail panel, in addition to the standard elements contained in all panel headers as described in the Panels tab will include additional controls for search navigation, zooming, and ribbon mode controls as displayed and described below. For more information on search-oriented functions mebtioned below, see the Search tab on this page.

Here is an example of the detail panel header for the Primary Detail panel with the search mode in both axes and in the both axis normal view versus one of the ribbon views. More information about the various icons and their relation to these settings can be found in the table below.

Axis Labels

While row and column matrix labels are never displayed on the summary panel, whether or not they are displayed in a detail panel depends on the screen space avaiable in the browser for a specific detail panel.

Making Selection on the Detail Panel

Selecting rows and/or columns in the heat map is useful because operations like copy to clipboard or link out functions may be performed on selections.

There is only one set of selections for an NG-CHM. All detail panels and plug-in panels will reflect this single set of selected data.

Rows or columns can be selected through a search or may be selected by clicking on a row or column label. To select multiple labels use shift-click to select a block of labels or control-click to individually select multiple labels. When labels are selected, you can right click on one of them to access a pop-up menu of actions that can be performed on the selected labels. For advanced maps, a variety of context specific link out options may be available.

Drag selection is also possible. On the Detail Panel hold down shift and the left mouse button while dragging the mouse pointer across the rows and columns you wish to select. Matrix data specific link out functions can be accessed by right clicking on the resulting green selection box in the Detail Panel.

Keystroke Shortcuts

In addition to using the mouse as described above, some keystroke shortcuts are available for controlling aspects of the summary and detail panels.