Chromoscape features
Selecting elements / Zoom controls / Selecting element types / Show only selected - show all / Tier buttons

As the size and complexity of genomic data sets grow, data visualization requirements become more complex. Chromoscape provides features enabling the user to extract relevant information from a large and complex data set. These features include the abilities to:

• Select elements to retrieve more information and/or modify the display.
• Zoom the view in and out.
• Selecting element types to display.
• Change the order of displayed element tiers.
• Graphically highlight framework-to-interval element relationships and vice-versa.
• Search for elements and locate them in the graphic.
• Retrieve the eGenome entry (details) for elements in the Web browser.
• Navigate the display with scrollbars and/or via the keyboard.
• Print graphics.

Detailed descriptions of Chromoscape application screen features can be found below, or by clicking on the topics listed above.

To select an element, click once on its label. It will be highlighted with a gray background and outlined in red. If you select an element in an off-framework tier, the corresponding interval bar is also highlighted in red. If you click on the interval bar, all of the elements localized to this interval are highlighted:

Hold the shift key down when you click in order to add the selected element(s) to the current selection. Once you select an element, you can get detail about it in the browser using the Detail button. (Shortcut: double click on the label.)

Window controls

When you select an element, information about it appears above the graphic on the left-hand side. Here is shown the results of selecting an element labeled "D1S239":

Chromoscape provides controls to zoom the display in and out. When views are initially displayed, they are sized to fit horizontally in the window. As a consequence, not all of the framework labels might be visible, and it might be difficult to narrow in a particular region of a display. The zoom controls allow you to expand the views horizontally, thus exposing more framework labels and enlarging the viewable area. For example, the 1000 centiRay map on the left is extremely compressed and not all framework markers are visible (although their corresponding tick marks are). By zooming the map, all framework markers within a 300 centiRay region come into view. Scrolling the map will reveal the other markers.

By default, Chromoscape displays intervaled elements. If there are tiers with intervaled markers, a button labeled Select tiers... appears below the graphic title. When this is pressed, a pop-up window (Marker Display) shows a checkbox for each tier. To display the elements in a tier, check the box; to hide them, uncheck it. In the example shown below, only the Polymorphisms tier is displayed.

The button labeled "Show Only Selected" is available when you have selected intervaled elements in a display. It removes all the other elements from view and shows only the ones that you have selected. Pressing "Show All" restores the hidden elements. This can be of considerable benefit in making large displays more manageable to view.

 

Several markers selected

After pressing "Show Only Selected"

Tiers can be moved by clicking on the arrows appearing to the right and/or left of their titles. In the example shown above, the Polymorphisms and Bundles tiers can be swapped with each other.

• Chromoscape overview
• Menu controls
• Mouse and keyboard controls
• Printing from Chromoscape
• Chromoscape troubleshooting