Each track has a set of attributes that varies depending on the track type. For example, alignment tracks have attributes that are specific to the display of the read alignments. Some attributes are common across track types. For example, all tracks have a track name.
Setting track attributes#
Many of the track attributes are also user settable:
To set a attribute value for a specific track, right-click on the track (either in the data panel or the track name) to bring up a pop-up menu that is specific to the track type.
Some attributes can be set on multiple tracks at the same time. First, select all the tracks of interest and then right click on one of them to bring up the pop-up menu. You can select multiple tracks either by using the normal multi-select mouse actions (e.g.
Ctrl-click on Windows;
Cmd-click on MacOS) or by clicking an attribute in the sample attribute panel to select all tracks tagged with that attribute value.
Select View > Preferences to change the default value for an attribute for a particular track type. Not all default values are user settable.
In some cases, attribute values can be set via actions in the main IGV menu.
Common track attributes#
To change the color for tracks displayed as a heatmap:
- Right-click the track and select Set Heatmap Scale... from the pop-up menu.
To change the color for tracks that are displayed as something other than a heatmap (e.g, bar chart, scatter plot, line plot, alignments):
- Right-click the track and from the pop-up menu select either Change Track Color... or Change Track Color (Negative Values or Strand)....
To change the height of selected tracks:
- Select Change Track Height... from the track pop-up menu.
To change the height of all tracks:
- Select Tracks > Set Track Height... in the main IGV menu.
To change the default height of tracks:
- The Tracks tab in View > Preferences has fields to set the default height for numeric/quantitative tracks and for feature/genome annotation tracks.
Tracks are assigned default names, typically based on the file name or the names of samples contained in the file.
If you have loaded sample attributes, you can specify an attribute to define the default track name:
- Enter the sample attribute name in the field Sample attribute key for track names in View > Preferences > Tracks.
To set a track name to a specific string:
- Right-click the track, then select Rename Track... in the pop-up menu. You can only rename one track at a time.
The track names are displayed in a panel to the left the track data, and to the left of the sample attribute panel if it is displayed.
To hide the name panel, unselect View > Show Name Panel.
To resize the name panel, select View > Set Name Panel Width...