Changing the Display

You can override IGV's default display options in several ways:

  • Use the track pop-up menu to change the appearance of selected tracks.
  • Use the Preferences window to set display preferences for all tracks.
  • Use the Color Legends window to set the default data range and color for heatmaps, which IGV uses to display copy number, gene expression, RNAi, methylation, LOH, and mutation data (Table 2).
  • For IGV and segmented (SEG, CBS) data files, add a type line to the data file to override the default data type associated with the file format and thus the default display options for the data.
  • Add a track line at the top of a data file to specify the display settings for the data.
  • Override the default display settings by including display attributes in the sample information file. Note that changes made with this method take precedence over the defaults prescribed by a #type line.  

This section describes a few commonly used display options that apply to all (or most) tracks: graph type, data range, track color, track height, and track names. For information about how to load and display specific types of data, see Viewing Data. For a complete list of display options, review the options available in the pop-up menus, Preferences window, Color Legends window, and the menu bar (View and Tracks menus).

Graph Type

Most tracks are displayed using one of four graph types (the following graphs show the same data):

Heatmap:  
Bar chart:  
Points (Scatter plot):  
Line plot:

IGV determines the default graph type for a track as described in Default Display.

To change the graph type of selected tracks:

  • Right-click a track and select a graph type from the pop-up menu.

Data Range

The data range for a track provides the minimum, baseline, and maximum value for the graph, and also whether the scale is linear or logarithmic. IGV determines the default data range for a track as described in Default Display.

To change the data range for selected heat map tracks:

  • Right-click a track and select Set Heatmap Scale from the pop-up menu.  The heatmap scale can be set per track.

To change the data range for other selected tracks:

  • Right-click a track and select Set Data Range from the pop-up menu.

Changing the data range can significantly affect the data display: 

minimum, baseline, maximum Result
 0,0,3  
-1.5,0,1.5  
 -5,0,5  

Track Color

To change the track color for selected heat map tracks:

  • Right-click a track and select Set Heatmap Scale from the pop-up menu.

To change the track color for tracks that are displayed as something other than a heatmap (i.e., bar chart, scatter plot, or line plot):

  • Right-click a track and from the pop-up menu select either Change Track Color (Positive Values) or Change Track Color (Negative Values).

Track Height

To change the height of selected tracks:

To change the height of all tracks:

  • Select Tracks>Set Track Height and enter a value.

To fit the data to the window:

  • Select Tracks>Fit to Window.
    IGV displays all tracks. If necessary, it sets the track height to 1 pixel and scrolls the data.

Track Names

By default, IGV displays track names to the left of the attribute panel. Legibility of the track names depends on track height; for example, track names will not be legible when track height is 1 pixel).

To select the attribute IGV uses as the track name:

To display the track name as a track label:

To rename a track:

  • Right-click a track or a track name, then select Rename Track in the pop-up menu.

You can only rename one track at a time. You can preserve track name changes only by saving the session.

Viewing Options for the Feature Track

There are 3 different options for viewing the feature track.  These allow you to display overlapping features, such as different transcripts of a gene, on one line or multiple lines

To change the view of the feature track, right-click on the feature track and select one of the options:

Collapsed

Squished

Expanded