The Bird's Eye View function visualize quantitative data on a whole genome scale. Almost all types of quantitative data in this Browser can be displayed in such a way, including:
The only type of track not supported is read density of custom BAM track, which usually contains huge amount of data and genome-wide data processing would be prohibitive.
But user can work around by converting the read alignment into density data using bedItemOverlapCount
in UCSC Kent Source Tree, displaying it as custom bigWig track, and running Birds' Eye View on it.
Primarily, Bird's Eye View is used to obtain whole-genome view of a heatmap track. On genome heatmap, right click on a track of interest, and select the option in menu:
The Bird's Eye View will be displayed in a new panel:
In the panel, pairs of wiggle plot and chromosome ideogram are made for all chromosomes. The wiggle plot is made from track data just selected.
If an interesting region is spotted, you can zoom into it by dragging on the chromosome ideogram graph:
Once a region is selected, the Bird's Eye View panel is dismissed and the Browser is updated to show data around selected region.
To bring back Bird's Eye View panel, click "eye icon" in floating toolbox:
Right click on the wiggle plot to get a context menu:
Select wrench option to open the configuration panel in floating toolbox:
The panel contains identical set of options as the heatmap track configuration panel. Please refer to chapter of heatmap track for details.
For quantitative genomic feature tracks this is simple. Take GC percent track as example, right click on the track image and select menu option, the whole-genome GC percent profile will be displayed in Bird's Eye View panel:
For genomic feature tracks with positional data, turn it into "density" mode first:
Then choose "Bird's Eye View" option in the context menu on the density track:
Following example is whole-genome Alu/SINE element density profile:
You can further configure the track's appearance via steps described in previous section.
This function has been briefly mentioned in chapters on pairwise comparison and hypothesis test. After the statistical function has been turned on, right click on track image and select menu option:
The analysis will be computed using data over entire genome and results be rendered in Bird's Eye View panel:
Tracks participated in the test or comparison can be viewed by clicking "data icon" in the panel:
In this table each row is one heatmap track. Different background colors indicate which group the tracks belong to in the test or comparison. By checking an empty checkbox, the heatmap track can be displayed along side the log-ratio track or P-value track:
Click the wrench icon on top-left corner of panel:
The configuration panel will be displayed below the icon:
The plot width of Bird's Eye View can be modified via first drop-down menu, which is plot width of longest chromosome in pixels. All the other chromosomes will scale accordingly. Once you change this, the Browser need to re-compute data for the tracks before the plot updates.
Apart from this option, all the other options won't involve server interaction and can take effect immediately.
From these options, you can change height of chromosome ideogram graphs, or hide them completely:
You can also change view box height which controls how many chromosome could be displayed.
Last modifed: 1/4/2012