Cytoscape WikiUse Case Name : ... |
For Feature : ... |
Editors: ... |
Summary
Step-by-Step User Action
- Select two or more nodes
- Choose "Group Paralogs" or just “Group” (don’t know how specific this needs to be for the user) from a context menu, main menu or toolbar
- Automatically view collapsed view of group with default label (editable)
- Be able to expand group as vertically stacked set of nodes by a very simple mechanism (e.g., click on a plus/minus icon)
a. perhaps other restricted views of the children will be allowed: i. horizontal stack i. block (e.g., 2x2, 3x4) i. overlapping "clump" of nodes packed into a some defined circular area
- Be able to destroy group
- Be able to expand-all or collapse-all groups in a given network
- Same as 3-6 above
Visual Aides
Requirements for Cytoscape
- The Group API can handle this one in terms of create, expand, collapse and destroy
- A simple GUI for create, expand, collapse and destroy should be sufficient. Specific semantics for paralogs may not be necessary.
- Need to add simple layout/alignment algorithms for stacking children vertically in expanded view
- Need to support the storage of groups in a pathway file format. xGMML and GenMAPP's GPML?
Importance
Other Examples
- Simple, intuitive examples of expand and collapse can be found in directory tools/explorers that let you click on an icon (e.g., a triangle or plus/minus) to expand and collapse the view.
- Illustrator and other such programs have a grouping function that mimics the restriction on children once a group is formed. You cannot move the children relative to each other, for example. If you want to treat them independently, you have to ungroup.