Format Heat Map
The purpose of the Format Heat Map screen is to provide users with a set of tools, displayed in different sub-panels within the configuration panel, for formatting various aspects of heat map display. These tools include: Matrix Colors/Breaks, Heat Map Display, Labels and Attributes, and Heat Map Gaps. Each of the panels containing these tools may be toggled open using the Format Tasks drop-down at the top of the configuration panel.
The Matrix Colors tool enables changes to colors and threshold values that assign a color to each cell in the heat map body. The Heat Map Display tool allows users to change the visibility, size, color, and length of objects (e.g. dendrograms, labels, grids, etc...) displayed on the heat map. The Labels and Attributes tool permits the addition of label types for linkouts, top items, and heat map level attributes to the heat map. Finally, Heat Map Gaps (an advanced feature) allows users to place gaps into the heat map display based upon location or cluster.
The results panel of this screen contains a rendering of the Summary side of the actual NG-CHM Viewer application page. The summary heat map is visible along with any applied covariate bars, top items, gaps, and hierarchical dendrograms.
Format Screen Sub-Panels
Configuration Controls
| Configuration Item | Description of Function |
|---|---|
| Show Advanced Features | Check this box to expand builder options to show advanced system features. Un-check the box to see a streamlined set of standard builder options. |
| Format Tasks | Select the type of heat map formatting task that you wish to perform. Available types include: Matrix Colors/Breaks, Heat Map Display, Labels and Attributes, Heat Map Gaps |
| Threshold | Enter/Edit a value for a given matrix threshold. Sub-panel location: Matrix Colors/Breaks. |
| Color | Select a color, using a color picker dialog, for display of data points that fall within a given threshold in the matrix. Sub-panel location: Matrix Colors/Breaks. |
| Missing Color | Select a color, using a color picker dialog, for display of missing values in the matrix. Sub-panel location: Matrix Colors/Breaks. |
| Threshold Add Button | This green “plus” button can be pressed to add a new threshold below the selected item. Sub-panel location: Matrix Colors/Breaks. |
| Threshold Remove Button | This red “minus” button can be pressed to remove an existing threshold. Sub-panel location: Matrix Colors/Breaks. |
| Pre-defined Palettes | The See Palettes button displays a pop up dialog (see description in Covariate screen section above) where the user may select from pre-defined color palettes for their matrix bar or create new ones. |
| Selection Color | Select a color, using a color picker dialog, for the display of the box that highlights selection location in the NG-CHM Viewer. Sub-panel location: Heat Map Display. |
| Gaps Color * | Select a color, using a color picker dialog, for the display any heat map gaps. Sub-panel location: Heat Map Display. |
| Grid Color | Select a color, using a color picker dialog, for the grid displayed on the detail side of the heat map. Sub-panel location: Heat Map Display. |
| Show Grid | Choose (YES/NO) whether a grid will be displayed on the detail side of the heat map. Sub-panel location: Heat Map Display. |
| Summary Display Width | Select a display percentage for the summary side of the heat map view. Sub-panel location: Heat Map Display. |
| Show Dendrogram | Select if and where the row/column dendrogram will be displayed in the heat map view (where applicable). Sub-panel location: Heat Map Display. |
| Dendrogram Height | Select the display height for the a row/column dendrogram (where applicable). Sub-panel location: Heat Map Display. |
| Maximum Label Length | Select the maximum displayed label length for row/column labels in the heat map view. Sub-panel location: Heat Map Display. |
| Trim Label Text | Select the location (beginning/middle/end) to abbreviate row/column labels that exceed the maximum label length. Sub-panel location: Heat Map Display. |
| Label Type | Select a label type for all row/column labels. Label type is used to link labels to active plug-ins defined for the heat map. Sub-panel location: Labels and Attributes. |
| Top Label Items * | Enter a comma-delimited string of row/column labels as top items. These items will be highlighted, for easy access, on the summary side of the heat map view. Sub-panel location: Labels and Attributes. |
| Heat Map Attributes * | Enter a comma-delimited list of colon-separated key/value pairs as additional attributes for this heat map. Sub-panel location: Labels and Attributes. |
| Gap Method * | Select a row/column gap method (by location or cluster) for gaps to be added to the the heat map. Sub-panel location: Heat Map Gaps. |
| Gaps By Location * | Enter a comma-delimited list of numeric gap locations. A row/column gap will be placed in the heat map at each of these locations. Sub-panel location: Heat Map Gaps. |
| # of Clusters * | Enter a numeric value for the the number of hierarchical clusters to break the heat map into using gaps. Sub-panel location: Heat Map Gaps. |
| Gap Length * | Enter a numeric value for the width (in rows/columns) of all row/column gaps displayed in the heat map. Sub-panel location: Heat Map Gaps. |
| Apply Button | Press this button to apply any formatting changes, rebuild, and reload the displayed heat map. |
| Prev Button | Press this button to return to the Process Covariates screen. |
| Next Button | Press this button apply any formatting changes made and proceed to the Interactive Heat Map screen. |
| * - denotes advanced feature configuration options. |
Select Custom Color Palette
This popup window opens when the user selects the See Palettes button on the Format Heat Map screen. It allows the user to select from any pre-defined color palettes that have been set up for the main matrix bars in the system. The user may pick from the available palettes by selecting from the box and pressing "select" or may choose to create their own custom palette using the "Create New Palette" button. Options on this panel will vary depending upon the Color Type of the covariate.
Create Custom Color Palette
This popup window opens when the user opts to create their own color palette. It allows the user to create their own color palette by adding/removing breakpoints and colors. Newly created palettes will then be available in the Select Custom Palette popup window.
Next Step
Once all heat map format changes have been applied, the user is ready to view their dynamic heat map in the NG-CHM Viewer and may move on to the final step in the NG-CHM Builder heat map creation process: Interactive Heat Map.