Rendering

Rendering allows a user to specify special colors, fonts, and other visual effects that will be applied to terms in a ontology editor panel that match a particular filter. Renderers can be applied in any Ontology Tree Editor or Graph Editor panel, and each panel can have different renderers. See the page about coloring by namespace for an example of how to use rendering.

To create a new renderer, click the wrench icon on the panel where you want the rendering effects to appear. Choose the "Term Renderers" or "Link Renderers" tab. Click the button to bring up a filter panel, then specify the filter criteria or load a saved filter (see Building Filters for how to do this).

Next, specify one or more visual effects to apply to matching terms. To apply the new renderer to the panel, click the check mark to complete panel configuration.

With the settings shown in the screenshot below, the ontology editor panel will draw any term whose name contains "activity" in red:

A ontology editor panel can have any number of renderers at the same time.

Specifying Renderer Options

Renderers can apply several different visual effects to matching terms. The available effects are different for term filters and link filters.

In general, to apply a visual effect, select the checkbox next to it. If a visual effect is configurable, a configuration control will appear next to the checkbox once it is selected. A renderer may apply several visual effects to a matching term.

Term Renderer Effects

Term renderer effects change the way a term name is displayed in the ontology editor panel. The following renderer effects are available for term filters:

• Foreground Color - The "Foreground Color" effect changes the color of the text displaying terms that match the filter. If the "Foreground Color" checkbox is checked, a set of controls will appear next to the checkbox, allowing you to configure the color that will be applied to matching terms.
  • Simple coloring - This is the most commonly used color renderer. If the "Simple coloring" box is checked, matching terms will appear in the selected color. To choose a different color, click the "CHANGE" button. A color selection window will appear where you can choose a different color for matching terms.
  • Heat map coloring - Some OBO-Edit search criteria are numeric rather than text based (e.g. Parent Count). You can use the configurable "Heat map coloring" to create a graduated coloring based on numeric search criteria. If the "Heat map coloring" box is checked, additional controls appear that allow you to configure the color gradient.
    • Min color, Max color, and Blank color - The "Min color" and "Max color" buttons allow you to select the colors for the minimum and maximum ends of the gradient, respectively; the "Blank color" button lets you specify the color to use for missing values. Each button makes the color selection panel appear.
    • Criterion - This selector lets you choose which numeric criterion to use to generate the heat map. In OBO-Edit 2.0, the available options are Parent Count and ISA Parent Count (more may be added in future versions of OBO-Edit).
    • Minimum Value and Maximum Value - These selectors let you specify the minimum and maximum values for the gradient. The "<auto-calculate>" option automatically determines the color depending on which matching terms are selected; "<enter constant>" lets you enter your own maximum and minimum values; "Max parent count" and "Min parent count" use the maximum and minimum values in the ontology.
• Background Color - The "Background Color" effect changes the background color of terms that match the filter. If the "Background Color" checkbox is checked, a set of controls will appear next to the checkbox to configure the background color that will be applied to matching terms. The color controls work the same way as for "Foreground Color", described above.
• Font Face - The "Font Face" effect changes the typeface of terms that match the filter. If the "Font Face" checkbox is checked, a dropdown list of available fonts will appear next to the checkbox. Select the font you would like to apply to matching terms.
• Font Size - The "Font Size" effect changes the type size of terms that match the filter. If the "Font Size" checkbox is checked, a text field with arrows appears next to the checkbox. Type the desired text size into the text field or use the arrows to increment the size up or down.
• Bold - The "Bold" effect makes matching terms appear in a bold typeface. There are no special configuration controls for this effect.
• Italic - The "Italic" effect makes matching terms appear in a italic typeface. There are no special configuration controls for this effect.
• Underline - The "Underline" effect makes matching terms appear undelined. There are no special configuration controls for this effect.
• Strikeout - The "Strikeout" effect makes matching terms appear struck out, i.e. with a horizontal line through the type. There are no special configuration controls for this effect.
• HTML Code - This checkbox allows you to specify OBO-Edit renderers in HTML code. See HTML Rendering for details.

Link Renderer Effects

Link renderer effects change the way the arrow between a term and its parent () is displayed in the ontology editor panel. The following renderer effects are available:

• Foreground Color - The "Foreground Color" effect changes the color of the link arrow for links that match the filter. If the "Foreground Color" checkbox is checked, color selection controls will appear next to the checkbox. See Term Renderer Effects above for a description of the color selection controls.
• Line Width - The "Line Width" effect changes the thickness of the link arrow line. If the "Line Width" checkbox is checked, a text field with arrows will appear next to the checkbox. Type the desired line width (in pixels) into the text field or use the arrows to increment the size up or down.
• Line Type - The "Line Type" effect changes the way the link arrow line is drawn. If the "Line Type" checkbox is checked, a dropdown box will appear next to the checkbox showing the available line types. The available options are "SOLID-LINE", "DASHED_LINE", and "ZIGZAG_LINE".

Multiple Renderers at Once

Any number of renderers may be applied to a ontology editor panel at once. If a term matches multiple renderers, OBO-Edit will try to merge the renderer effects to display as much information as possible.

OBO-Edit can merge renderer effects of different types. If one renderer wants to make a term red, and another wants to make a term bold, OBO-Edit will show the term in red and in bold. But OBO-Edit cannot merge effects of the same type. If one renderer wants to make a term red and another wants to make the term blue, OBO-Edit will only display a single color.

When two renderers specify two different values for the same effect, OBO-Edit chooses the value from the most recently added renderer.

Therefore, if you plan to use several renderers at once, it is usually a good idea to use a different type of renderer effect for each renderer. That way it is easy to tell if a term matches multiple renderers.

Removing Renderers

To remove a renderer, click the wrench icon to open the configuration screen, and choose the "Term Renderers" or "Link Renderers" tab. Select the renderer you want to remove, and click the button to remove it. Click the check mark to finish and exit configuration.