Process Covariates
Covariate bars are generated by applying a covariate file to the heat map. They can contain information related to either rows or columns in the data matrix. Covariate bars contain discreet classification data (e.g. sub-type) or continuous data (e.g. age). Column covariate bars, appear in the NG-CHM Viewer at the top of the heat map. Row covariate bars to the left of the map. Discrete covariate bars are displayed as a color bar with different colors associated with each discrete category in the data. Continuous covariate bars can be displayed as a color bar, scatter plot, or bar plot with the color varying in shade between the upper and lower boundaries of the data.
The first step in processing a covariate bar in the NG-CHM builder is to select a covariate file and enter values for display Name, Position (data axis), Color Type (discrete/continuous). A covariate file can be a text or .XLS file. Each row in the file must contain 2 data values: A key value and a data value. These must be separated by a tab in a text file and reside in separate columns in an .XLS file. All key values must match labels found on the data matrix in the appropriate row/column. Once the bar has been added, the user may further configure the display of the bar.
Using controls located on the configuration panel of the Process Covariates screen, users may add, remove, and reorder covariate bars as well as modify the appearance of each covariate bar. Select the covariate bar you wish to customize from the Covariates drop-down and the user may then change color settings, size, display type, and whether it should be displayed. For continuous covariate bars, you can also choose an alternate presentation option of barplot or scatter plot. When either of these are selected, the user will be shown a panel containing controls specific to these bar representations.
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 and hierarchical dendrograms.
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. |
| Covariates | Select an existing covariate bar, by name, to edit. |
| Add | Press this button to add a covariate bar to the heat map. An add covariate panel will be displayed allowing the user to upload a covariate to the heat map. |
| Remove | Press this button to remove a covariate bar from the heat map. A remove covariate panel will be displayed allowing the user to remove the bar from the heat map. |
| Reorder | Press this button to reorder the display of covariate bars on the heat map. A reorder covariate panel will be displayed allowing the user move covariate bars around, using graphical controls, to change their display order. |
| Select File Button | Displayed in the Add Covariate panel. Press this button to select a covariate file for the heat map. |
| Bar Name | Enter the label that you want to appear displayed with the covariate bar. |
| Position | Select the axis (row/column) upon which the covariate bar will appear in the heat map. |
| Bar Type * | Select a display type for the covariate bar. Bar Type may only be changed for continuous color type covariate bars. Available bar types include: color plot, bar plot, and scatter plot. |
| Height | Enter a value, between 1 and 99, for the display height of the covariate bar. |
| Show | Choose whether covariate bar will be displayed (or hidden) on the heat map. |
| Color Type | Select the color type (continuous/discrete) for the values in the covariate bar. |
| Color | Select a color, using a color picker dialog, for a given category on the covariate bar. A color picker will appear for each category in the covariate. |
| Missing Color | Select a color, using a color picker dialog, for missing values on the covariate bar. |
| Pre-defined Palettes | The See Palettes button displays a pop up dialog (see below) where the user may select from pre-defined color palettes for their covariate bar or create new ones. |
| Lower Bound * | Select a lower boundary value for the scatter/bar plot range. This control only appears for continuous covariate bars for which the user has selected the bar type of Bar Plot or Scatter Plot. |
| Upper Bound * | Select an upper boundary value for the scatter/bar plot range. This control only appears for continuous covariate bars for which the user has selected the bar type of Bar Plot or Scatter Plot. |
| Foreground Color * | Select a foreground color, using a color picker dialog, for scatter/bar plot display. This control only appears for continuous covariate bars for which the user has selected the bar type of Bar Plot or Scatter Plot. |
| Background Color * | Select a background color, using a color picker dialog, for scatter/bar plot display. This control only appears for continuous covariate bars for which the user has selected the bar type of Bar Plot or Scatter Plot. |
| Apply Button | Press this button to apply any covariate changes, rebuild, and reload the displayed heat map. |
| Prev Button | Press this button to return to the Cluster Matrix screen. |
| Next Button | Press this button apply any covariate changes made and proceed to the Format 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 Covariate screen. It allows the user to select from any pre-defined color palettes that have been set up for covariate 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. Options on this panel will vary depending upon the Color Type of the covariate.
Next Step
Once all covariate processing has been performed, the user may move on to the next step in the NG-CHM Builder heat map creation process: Format Heat Map.