View Operations

Peter Kerpedjiev edited this page Sep 4, 2017 · 5 revisions

Views

Views are visible units with their own x and y scales. Every track within a unit shares the same view-wide x and y scales. 2D tracks in the middle use both the view-wide x and y scales. Horizontal tracks use the view-wide x scale and ignore the y. They can define their own y scale (as in Line tracks) that scales values in the track or they can simply display information without a y scale (gene annotations). Vertical tracks ignore the view-wide x scale and can define their own.

All tracks share the same scaling factor.

Adding new views

New views are created by clicking the copy view icon on the right side of the view header. The newly created view will be a copy of the view on which the icon was clicked. When created, it will try to place itself at nearest available position moving left to right, top to bottom.

Closing views

Views are closed by clicking the close view icon. The vertical space which is occupied by a view can then be compacted by views below it.

Cross-view operations

Cross view operations involve transferring or linking parameters (such as scaling factor and location) between two separate views. They are always initiated from the view settings menu and always involve the selection of a target view. When a cross-view operation such as taking the zoom level is initiated, a target view selector appears as green overlay. Hovering over different views moves the target view selector to that view. Clicking on a target performs the operation between the source view (the one which initiated the operation) and the target view (which was selected).

View synchronization

While scales between views are generally independent, it is possible to synchronize the axes of one view with another.

Take zoom from

Taking the zoom from a different view sets the scaling factor of this view to that of the target view. Both views remain centered on the same point that they were centered on before the operation.

Take location from

Taking the location from a different view sets the center of this view (along both the view-wide x and y axes) to the the center of the target view.

Take location and zoom from

Taking the location and zoom from a different view centers and zooms this view on the same location (e.g. same center point) as the target view.

View linking

Having independent view-wide x and y scales is useful for displaying different regions in different views, but there are situations when we may want to link (lock) scales between views. This operation maintains a constant difference between either the center points or scale factors of two views. This constant difference is equal to the difference in the parameter (center point or scale factor) at the time of linking.

It is entirely possible to link more than two views. The pairwise differences in parameters are maintained between all of the members of the zoom group.

Linking views by zoom level (scale factor)

Views linked by zoom level maintain a constant zoom separation. When one view is zoomed, the other linked views follow. The locations remain free and panning is unconstrained between views.

Linking views by location (center point)

Views linked by location maintain a constant separation of their center points. They may be scaled independent of each other but the difference in center point location remains constant. Note that zooming often modifies the center point so zooming operations may appear to move both views but this is simply a byproduct of the ability to zoom into points away from the center.

Linking views by zoom and location

Views linked by zoom level and location always maintain a constant separation between both parameters. Zooming in one zooms or moves in the other.

Unlinking

Any parameter linking can be removed from the view settings menu.

Syncing and linking at same time

A common operation is taking the zoom level and location from a different view and linking their zooms and locations. This is useful when one wishes to compare identical locations in multiple samples. While this operation can be accomplished by first taking the zoom and location and then linking the zoom and location, we've also included a convenience menu option which performs both operations with one action.

Searching for a gene or genomic coordinate

It's possible to search for a particular locus using the genome position search box:

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If the genome position search box isn't visible, it can be enabled by toggling it in the view config menu:

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