Cytoscape Wiki|
Size: 424
Comment:
|
Size: 1542
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 6: | Line 6: |
| Since the basic file format for 2.3 and later is ''Session (.cys)'', we the save and load functions are now called import/export. | |
| Line 7: | Line 8: |
|
* New * Network * Empty Network - '''''Cytoscape Editor''''' will be called from here. * From selected nodes, all edges (Ctrl-N) * From Selected nodes, selected edges (Shift+Ctrl-N) * Session - Clean current workspace (networks and attributes) and start a new session. * Save - Save current session into a CYS file. Overwrite existing session file. * Save As... - Save the session with new name. File chooser will pop-up. * Open - Open the session file. Current session will be lost (dialog box will appear). * (Separator) * Import * Network (Ctrl-L) - Load network files: SIF, GML, or XGMML. * Node Attributes * Edge Attributes * Expression Matrix File (Ctrl-E) * Gene Ontology * Export * Network and Attributes as XGMML * Network as GML *(Separator) * Print (Ctrl-P) -- Print out current network as a graphic. * Quit (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear. |
|
| Line 20: | Line 43: |
|
|
* (Separator) |
Refactored Menu
The following is a tentative plan for the new menu bar.
File
Since the basic file format for 2.3 and later is Session (.cys), we the save and load functions are now called import/export.
- New
- Network
Empty Network - Cytoscape Editor will be called from here.
- From selected nodes, all edges (Ctrl-N)
- From Selected nodes, selected edges (Shift+Ctrl-N)
- Session - Clean current workspace (networks and attributes) and start a new session.
- Network
- Save - Save current session into a CYS file. Overwrite existing session file.
- Save As... - Save the session with new name. File chooser will pop-up.
- Open - Open the session file. Current session will be lost (dialog box will appear).
- (Separator)
- Import
- Network (Ctrl-L) - Load network files: SIF, GML, or XGMML.
- Node Attributes
- Edge Attributes
- Expression Matrix File (Ctrl-E)
- Gene Ontology
- Export
- Network and Attributes as XGMML
- Network as GML
- (Separator)
- Print (Ctrl-P) -- Print out current network as a graphic.
- Quit (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear.
Edit
Data
Select
View
Formerly called Layout and Visualization.
Plugins
List of loaded plugins will be displayed here. Same as 2.2.
Help
Basically, this is same as 2.2.
- Contents (F1)
- Context Sensitive (Shift+F1)
- (Separator)
- About