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Change Display Options

IGV offers several display options for tracks. As an example, this tutorial modifies the display of the loaded copy number data to match the visualization shown in Figure 2a of Beroukhim et al. (2007).

Data as it appears in the paper:

 

Data as it appears in IGV after modifying the display:

 

Zoom Out

To zoom out to the whole genome, click the whole genome view icon:

Modify Track Height

To modify the track height:

  • Select Tracks > Fit Data to Window.

Sort the Tracks

The figure in the paper sorts the tracks by diagnosis (the value of the DIAGNOSIS attribute). To sort the tracks by data type (expression vs. copy number) and diagnosis (primary vs. secondary vs. other gliomas):

  1. Select Tracks > Sort Tracks. IGV displays the Sort window.
  2. Sort by Data Type and then Diagnosis by selecting those attributes:
  3. Click OK to sort the tracks:

Remove the Gene Expression Data

The figure in the paper shows only the copy number data. For the tutorial, you loaded both gene expression and copy number data. To remove the gene expression data:

  1. Right-click the DATA TYPE attribute for any gene expression track to select all tracks that have been labeled with this attribute (that is, it selects all the gene expression tracks). IGV displays a context menu.
  2. Click Remove Tracks in the context menu. IGV displays a list of all tracks that have that attribute value.
  3. Click Yes to remove the tracks.
  4. Select Tracks > Fit Data to Window.

Filter the Tracks

The figure in the paper shows only the gliomas. At the moment, you are displaying all of the copy number data. Hover over the Type attribute to see the tumor type of the samples.

To apply a filter that displays only the gliomas (Type = Glioma) and hides the normals (Ploidy(Numeric) ≠ 2):

  1. Click Tracks>Filter Tracks. IGV displays the Filter Tracks window.
  2. Define a filter that displays the gliomas (Type is equal to Glioma):
    1. Select Type from the first drop-down list.
    2. Select is equal to from the second drop-down list.
    3. Enter glioma into the text box (third from the left).
    4. Click the plus (+) button to add a second filter.
  3. Define a filter that hides normals (Ploidy(Numeric) is not equal to 2).
  4. Select the check box 'Match all of the following' at the top of the window to combine the filter criteria using a logical AND (Type is equal to Glioma AND Ploidy(Numeric) is not equal to 2):
  5. Click OK to apply the filter. The display now resembles the visualization shown in Beroukhim et al. (2007):

Group the Tracks

The tracks are sorted by diagnosis (the DIAGNOSIS attribute). Grouping the tracks by attribute makes it easier to see the tracks associated with each attribute value. As an example, group the tracks by diagnosis:

  1. Select Tracks>Group Tracks. IGV displays a drop-down list of attributes.
  2. Select DIAGNOSIS and click OK. IGV groups the tracks by diagnosis.

To ungroup the tracks, select Tracks>Group Tracks and select None from the attribute list.