Default Display

When you load genomic data, IGV displays the data in horizontal rows called tracks. Typically, each track represents one sample or experiment. For each track, IGV displays the track identifier, one or more attributes, and the data.

When loading a data file, IGV uses the file extension to determine the file format (see File Formats), the file format to determine the data type (Table 1), and the data type to determine the track default display options (Table 2).

Table 1. File Format Determines Data Type
File Format	Data Type
CBS, CN, MAF, SEG, SNP, VCF	Copy number
LOH	LOH
GCT	Gene expression or RNAi
GISTIC	GISTIC data
RES	Gene expression
BAM, bam.list, Goby files, PSL, SAM	Sequence alignments
BED, genePred, GFF, GFF3	Genome annotations
MUT	Mutation
GWAS	Genome-wide association study data
IGV, WIG, HDF5 file not created with alignment processor, bedgraph	Other
Cytoband, FASTA	Not applicable. Cytoband and sequence files for an imported genome.

Table 2. Data Type Determines Display Options
Data Type	Default Graph Type	Default Data Range	Default Colors
Copy number	Heatmap	-1.5 to 1.5	Blue to red
Gene expression	Heatmap	-1.5 to 1.5	Blue to red
Chip	Bar chart	None, data is autoscaled	Blue
DNA methylation	Heatmap	0 to 1 (methylation score)	Green
Allele-specific copy number	Heatmap	-1.5 to 1.5	Blue to red
LOH	Heatmap	-1 to 1	Blue = LOH (1) Yellow = Retained (0) Red = Conflict (-1)
RNAi	Heatmap	-3 to 3	Red to blue
GWAS	Scatter plot	None, data is autoscaled	Chromosome colors
Other	Bar chart	None, data is autoscaled	Blue

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:
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. 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:

Use the track pop-up menu.

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:

Use the Tracks tab of the Preferences window.

To display the track name as a track label:

Use the Charts tab of the Preferences window.

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

Expression Data

File Formats

For expression data, use the GCT file format. This a tab-delimited format that contains a row for each probe set ID (or gene), a column for each sample, and expression values for each feature in each sample.

Display Notes

By default, IGV displays expression data as a blue-to-red heatmap where the data range is -1.5 to 1.5. If loaded expression data appears in tracks colored all red, check the data values and modify the data range as necessary.
To change track display options, use the track pop-up menu. The commands that appear in the pop-up menu are those relevant to any data track.

Genomic Locations for Probes

To display expression data, IGV must first map the probe set IDs named in the expression data file to their genomic locations. IGV displays data for all of the probes that it can map to genomic locations. If none of the probes in the file can be mapped, IGV displays an error message.

IGV determines the genomic locations for probes as follows:

If you use the delimiters |@ and | to specify the probe loci in the file (see the GCT file format), IGV uses the specified loci. Otherwise, it goes to the next step.
IGV searches all loaded annotation tracks for each probe. (This is the same as entering the ID in the first column [the Name column] of the file into the search box on the IGV tool bar and clicking Go.) If a probe is found, IGV displays the data at that location. Otherwise, it goes to the next step.
IGV searches its probe mapping files for each probe. If a probe is found, IGV determines the probe locus and displays the data at that location. Otherwise, it goes to the next step.
IGV uses its gene mapping files to map each probe ID to a gene symbol, determines the gene locus, and displays the data at that location.

Choose preferred mapping: By default, IGV uses its probe mapping files before its gene mapping files. If you prefer to map probes to genes, select the Map probes to genes radio button on the Probes tab of the Preferences window.

Probe Mapping Files

Probe mapping files map probe identifiers to chromosomal locations. They are compiled from source files provided by Affymetrix, Agilent, and Illumina. The Affymetrix and Agilent mapping files are split by species due to their large size. Separate mapping files are provided for human, mouse, and other (non-mouse, non-human) species. Human probe identifiers are mapped to hg18. Depending on the vendor, mouse probe identifiers are mapped to mm9 (Affymetrix), mm5 (Agilent) or mm8 (Illumina).

Following are links to the probe mapping files:

Gene Mapping Files

Gene mapping files map probe identifiers to gene identifiers. Following are links to the gene mapping files:

Sources for the Mapping Files

The probe and gene mapping files are compiled from source files provided by Affymetrix, Agilent, and Illumina. A list of the source files is available at http://www.broadinstitute.org/igv/resources/probes/data_sources_for_mapping.txt.

RNAi Data

IGV displays RNAi data similarly to expression data, with one exception: to facilitate analysis of hairpin scores, IGV provides a unique RNAi bar chart. To display the bar chart:

Right-click an RNAi track and select Bar Chart from the pop-up menu.

The following figure explains how to read the bar chart.

Hover over a track to view hairpin values.

Segmented Data

File Format

For segmented copy number data, use the SEG or CBS file format.

Display Notes

By default, IGV displays segmented data as a blue-to-red heatmap where the data range is -1.5 to 1.5. If loaded segmented data appears in tracks colored all red, check the data values and modify the data range as necessary.
To change track display options, use the track pop-up menu. The commands that appear in the pop-up menu are those relevant to any data track.

Gaps Between Segments

By default, IGV fills the gaps between adjacent segments by extending the segment endpoints. When zoomed in sufficiently, error bars indicate the gaps:

Alternatively, you can leave the gaps between the segments. In this case, the gaps appear gray:

To modify how gaps are displayed between adjacent segments set the "Join Adjacent CopyNumber Segments" option on the General tab of the Preferences window.

GWAS Data

IGV can display genome-wide association study (GWAS) data as a "manhattan plot", color-coded by chromosome. Data formats are describe here.

The plot represents the significance of the association between a SNP or haplotype and the trait being measured. The Y-axis shows -log10 transformed P values, which represent the strength of association.

The size of the data points in the plot and their height on the left-hand side of the data pane relate directly to their significance: the larger the point and the higher the point on the scale, the more significant the association with the trait. You can see the point size difference in the following screenshot of data on chromosome 1.

As in other parts of IGV, hovering over a data point allows you to see a pop-up containing the data specifically associated with that point. You can see the pop-up for the topmost data point in this image. Note that the point's position on the scale on the left is associated with its P value.

GWAS Pop-up Menu

The following commands appear in the pop-up menu for GWAS tracks:

Command	Description
Rename Track	Renames the track.
Remove Track	Removes the selected track from the display.
Set Data Range...	Changes the minimum, baseline, and maximum values of the scale used for the GWAS data.
Change Track Height...	Changes the display height of the track.
Color Scheme Chromosome color Single color Alternating color	Changes the display to use different color schemes for the chromosome color-coding. The chromosome color scheme (default) uses the colors defined in the legend in the Alignment tab of the Preferences window. The single color scheme changes all the chromosomes to display in a single color (blue by default). The alternating color scheme uses two colors (blue and gold by default) that alternate through the chromosomes.
Set primary color...	Set the color for the single color scheme and for one of the colors in the alternating color scheme.
Set alternating color...	Set the alternating color in the alternating color scheme.
Set minimum point size...	Set the minimum data point display size.
Set maximum point size...	Set the maximum data point display size.
Save image...	Save the current display as a PNG file.