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Cytoscape_3/UserManual
Operators ................................................................................................................. 54
Supported Functions ................................................................................................... 55
Pitfalls ..................................................................................................................... 57
Useful Tips ............................................................................................................... 57
The Formula Builder .................................................................................................. 57
A Note for App Writers ............................................................................................... 58
Navigation and Layout ........................................................................................................ 58
Basic Network Navigation ........................................................................................... 58
Other Mouse Behaviors ............................................................................................... 59
Automatic Layout Algorithms ...................................................................................... 60
Edge Bend and Automatic Edge Bundling ...................................................................... 70
Manual Layout .......................................................................................................... 72
Node Movement and Placement .................................................................................... 78
Visual Styles ..................................................................................................................... 78
What is a Visual Style? ................................................................................................ 78
Introduction to the VizMapper User Interface .................................................................. 83
Introduction to Visual Styles ........................................................................................ 85
Visual Attributes, Graph Attributes and Visual Mappers ..................................................... 88
Custom Graphics Manager ........................................................................................... 95
Visual Styles Tutorials ................................................................................................ 99
Advanced Topics ...................................................................................................... 115
Managing Visual Styles ............................................................................................. 120
Bypassing Visual Styles ............................................................................................. 121
Visual Property Dependencies .................................................................................... 121
Finding and Filtering Nodes and Edges ................................................................................. 123
Enhanced Search ...................................................................................................... 123
Filters .................................................................................................................... 123
The Select Menu ...................................................................................................... 128
Editing Networks ............................................................................................................. 129
Adding Node ........................................................................................................... 129
Adding Edge ........................................................................................................... 129
CytoPanels ...................................................................................................................... 130
What are CytoPanels? ............................................................................................... 130
Basic Usage ............................................................................................................ 131
Rendering Engine ............................................................................................................. 132
What is Level of Detail (LOD)? .................................................................................. 132
Linkout .......................................................................................................................... 133
Adding or Removing Links ........................................................................................ 134
App Manager .................................................................................................................. 136
What are apps? ........................................................................................................ 136
Installing Apps ......................................................................................................... 136
Managing your Installed Apps .................................................................................... 137
Cytoscape 3.0.1 User Manual
The Cytoscape User Manual copyright is owned by The Cytoscape Consortium, and is made available
under the same GPL license as Cytoscape itself: LGPL 2.1, the GNU Lesser General Public License, version
2.1, February 1999 available in text at http://www.gnu.org/licenses/lgpl-2.1.html.
Copyright (c) 2001-2013 The Cytoscape Consortium, 965 Windflower Way, San Diego, CA 92106 USA.
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