Track Options

Track Options

This section shows how to reorder tracks and change their rendering settings. You can use Mouse or keyboard for most of the actions shown in this section. Using keyboard shortcuts are more productive compared to doing all things with Mouse.

View Settings

Tracks could have Title, Axis and Legend.

You could turn on/off showing title, axis, legend and browser grid using Main Menu | View menu section.

Select Track

You can select the desired track using two ways:

• Using Mouse: Click on required track using Mouse Left Button

  

• Using Keyboard: Press ↓ or ↑ keyboard keys until the required track has been selected.

Clear Tracks Selection

Press Esc keyboard key to unselect all tracks.

Or you could use Main Menu | Edit | Clear Tracks Selection.

Rename Track

You can rename a track using two ways:

• Using Mouse:

  • Open track context menu (click on required track using Mouse Right Button) and select Title... menu item.

    

  • Change track title and press OK.

    

• Using Keyboard:

  • Select required track (using ↓ or ↑ keys)

    

  • Press Enter (or Return) keyboard key

    

  • Change track title and press Enter (or Return) to save changes or Esc to cancel.

Change Color

You can change track color using two ways:

• Using Mouse:

  • Open track context menu (click on required track using Mouse Right Button) and select Color... menu item.

  • Select new color in Choose a color dialog and press OK.

    

• Using Keyboard:

  • Select required track (using ↓ or ↑ keys)

  • Press Space to open track context menu

  • Select Color... menu item and press Enter (or Return).

  • Select new color in Choose a color dialog and press OK

    

Change Track Height

You can change track height using two ways:

• Using Mouse:

  • Open track context menu (click on required track using Mouse Right Button) and select Track Height... menu item.

  • Select new track height in pixels in Track Height dialog and press OK.

    

• Using Keyboard:

  • Select required track (using ↓ or ↑ keys)

  • Press Space to open track context menu

  • Select Track Height... menu item and press Enter (or Return).

  • Enter new track height in pixels in Track Height and press OK

    

Track AutoScale vs. Fixed Scale Modes

For signal tracks (BIGWIG or WIG) JBR auto-scales track signal value according to max and min value in visible range by default. The minimal value is 1 pixel; the maximum value is the track height. The auto-scale mode helps to compare signal shape for different tracks even if the signal is not normalized among the tracks.

E.g., at the screenshot, the max value is 2786.862, and the minimal value is 0.995.

Instead of auto-scale, you can manually set min, max signal value thresholds. It allows to get the same scale for any genome range, trim outlier values and do not scale noise in small ranges.

You can change min/max thresholds:

• Using Mouse:

  • Open track context menu (click on required track using Mouse Right Button) and select Scales Min... or Scales Max.. menu items.

  • Select new signal threshold in Scales Max / Scales Min dialog and press OK.

    

• Using Keyboard:

  • Select required track (using ↓ or ↑ keys)

  • Press Space to open track context menu

  • Select Scales Min... or Scales Max.. menu item and press Enter (or Return).

  • Enter new signal threshold in Scales Max / Scales Min and press OK

    

E.g., let's set scales maximum 300 and minimum to 0: Auto-scaled signal:

Changed scale signal:

To unset custom max/min scales use Autoscale action in the track context menu.

Remove Track

You can remove a track from the current session

• Using Mouse: Open track context menu (click on required track using Mouse Right Button) and select Remove Selected Track menu item.

  • Select new signal threshold in Scales Max / Scales Min dialog and press OK.

• Using Keyboard:

  • Linux/Windows: Alt + Delete / Alt + Backspace
  • MacOS: Option ⌥ + Delete

This action does not delete track file.

Show in Explorer / Finder

You can open track file in Explored (MacOS: Finder) using Show in Explorer (Show in Finder) track context menu item. This menu item is grayed for URL based tracks.

About Track

Information about track could be shown using About Track action in the track context menu. The about track content depends on track type.

E.g.:

• BIGWIG track

  

• Peaks tracks

  

Reorder Tracks

• Using Mouse:

  • Hold Control (Windows, Linux) or Command ⌘ (MacOS) keyboard key
  • Press and hold Mouse Left Button
  • Move mouse up/down and JBR will show track insertion position using the thick red line

• Using Keyboard:

  • Select required track (using ↓ or ↑ keys)
  • Move track up/down using Alt + ↑ / ↓ (Windows, Linux) or Option ⌥ + ↑ / ↓ (MacOS) keyboard keys.

E.g. move green track up:

• Before moving:

  

• Select green track and move it up:

  

• Result:

  

Keyboard shortcuts also allow moving a group of selected tracks.

Multiple Tracks Operations

Tracks reordering feature and context menu actions could be applied to selected tracks group.

Select Multiple Tracks

Two ways are possible:

• Using Mouse:

  • Click first track using Left Mouse Button

    

  • Hold Shift keyboard key

  • Click last track using Left Mouse Button

• Using Keyboard:

  • Select first track (using ↓ or ↑ keys)
  • Hold Shift and press ↓ / ↑ keyboard keys to select/deselect tacks

  

Add / Remove Track To Selected Group

To add/remove tracks to the selected group hold Control (Windows, Linux) or Command ⌘ (MacOS) keyboard key and click on track using Left Mouse button.

E.g.: let's add the last track to selection:

Result:

Context Menu Actions for Multiple Tracks

JBR highlights with red color and (*) menu items if selected tracks have different values for the menu item. E.g., selected tracks have different titles and colors, so we get Color...(*) and Title...(*) menu items.

Context actions change all selected tracks settings using the same value for all tracks. E.g., if you press Color...(*) and select green color, all selected tracks will become green. If tracks have different values, dialogs for changing values show the value of first track as a default choice. In the above example default choice for Color...(*) will be light blue.

BIGWIG Tracks Additional Actions

For BigWig tracks you could set signal log scale using context menu Scale item.

E.g.:

• Normal scale

  

• Log10 scale

  

BED-like Tracks Additional Actions

Region Color

If BED-like track file contains color assigned to each region you could choose whether to use colors provided by the file or use fixed color instead, use Region Color item in track context menu.

Region Label

Peak names are shown as region labels by default. If peak name column is missing or empty JBR will use show region scores instead.

You could choose whether to show region Score or Name using Region Label submenu in the track context menu.

E.g., region score is used instead of region name.

Region Score Column

BED format assumes that scores are stored in the fifth column. You could choose any other column using Region Score Column submenu. It could be useful if you know which column contains p-value or q-value and you'd like to visualize them in the browser.

Transparency as Significance Level

Usually, a score column is associated with peak significance level in BED-like files. The scores are not p-values (or q-values) but are values of some function applied to them. You could read about the meaning of score column in the documentation of the tool used to create your BED-like files. Typically, the higher the score, the more significant the value is. JBR could draw less significant peaks as transparent and more significant peaks as opaque.

JBR auto-scales transparency level according to the file scores distribution. By default the lowest bound for scaling is the min score (whole track), the highest bound is score 80th percentile (whole track). You could overwrite defaults using Scales Min... and Scales Max... context menu actions and reset scales using Autoscale action. Scores less than or equal to the lowest bound are almost transparent. Scores greater than or equal to the highest bound are opaque. Scores between the bounds get linearly scaled transparency levels.