Help: Using the Bucket, working with pathways

The Bucket

Introduction

Bucket icon The bucket allows the arrangement of pathways in a 3D setup.
The bucket consists of three levels:

  • Center
  • Bucket walls
  • Pool level
A contextual heat map and a parallel coordinates view show genes which are contained in the loaded pathways at the center and wall level. Genes inside the pathways are highlighted on mouse over. Short information on the gene is presented in an info area located near the tool bar. The selected gene is automatically queried in the embedded browser view (if opened).

Pathways can be directly loaded by using the drop down search field in the pathway tool bar. In addition it is possible to load pathways by using the search view or via the gene context menu (activated with a right-click on a gene).


Bucket

Navigation

Bucket navigation mode All views inside the bucket (pathways, heat map, parallel coordinates) can be rearranged in the bucket by using drag&drop. The user can simply grab the view by clicking (without releasing the button) the title bar of the view and move it to another position in the bucket (i.e. center, bucket wall, or pool). When the designated position is reached, the user has to release the mouse button. In the case another view is already at the designated position, the two views are switched.

Bucket navigation mode icon The navigation mode, which is accessible via the tool bar, is an alternative method for rearranging the views inside the bucket. It shows an overlay with arrows pointing in the designated moving direction. When the aimed direction is already occupied by another view, the views are switched.






Bucket zoom icon Bucket zoom The user can zoom into the bucket by either using the mouse wheel or by triggering the zoom action via the tool bar. The zoomed in mode of the bucket displays the center view in detail.

Bucket connection lines icon The connection lines icon allows the user to switch on/off the connection lines inside the bucket. The visual links support the identity visualization of a specific gene contained in different pathways.

Bucket reset icon Resetting the bucket throws away all previously loaded pathways. After a reset the bucket appears in its initial state with an empty heat map and a parallel coordinates view.





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website maintained by Marc Streit and Alexander Lex
last updated on 2010-07-29