Cytoscape WikiUse Case Name : Named List of Genes |
For Feature : Groups |
Editors: Alex Pico |
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Summary
Sometimes you want to be able to annotate a group of genes without being reflected in the view in any way, but rather just assigning a name to the group for reference or maybe selection (and subsequent attribute browsing, moving, new network or for a plugin, etc).
Step-by-Step User Action
Manual Selection
- Select two or more nodes
- Choose "form named group" from context menu
Add the newly named group to panel (CytoPanel_1: Groups?)
- Allow selection of group via panel
- Allow renaming the group and destroying the group
Attribute-based Selection
- Menu option: "Group by attribute"
- Select Attribute and value (or multiple values, including all values)
Add newly formed group(s) to panel (CytoPanel_1: Groups?)
- Same as 4 and 5 above
Visual Aides
In this application you can group objects to make future selections easier and to apply functions to all children of the group 
Requirements for Cytoscape
- The current Group API can already perform the create and destroy
- Need to add item to context menu for group selection
- Need to provide a panel to display the group names and some functionality
Can potentially use the Attribute selection GUI from Ethan's QuickFind (also used in BubbleRouter plugin)
- Need to support storing named groups in xGMML
Importance
This one seems low priority to me. I think this function will overlap with other more complex grouping use cases and won't require special attention. IOW, we'll get this functionality for free in the implementation of the other more specific use cases.
Other Examples
geWorkbench was mentioned at the hackathon: http://magnet.c2b2.columbia.edu/geworkbench.php
- Some turn-based strategy games have a similiar function, where you can select a number of characters (troops, tanks, orcs, whatever) and assign them to a group, allowing you to simplify the command structure (e.g., go attack that village). These groups can also be assigned to hotkeys for quick selection, for example.