Figure: Using the default Visual Style.
The vizmap.props File: All Cytoscape Visual Style settings are automatically loaded from a file called vizmap.props. The location of this file can be specified from the command line (-vp). If it is not specified through the command line, then Cytoscape looks for this file in the user’s home directory (in the ".cytoscape" directory). If you start Cytoscape for the first time, and you do not start it using one of the start-up scripts (cytoscape.sh or cytoscape.bat), then, a very simple visual style will be automatically created. When you exit Cytoscape, any modifications you made to the visual styles, and any new visual styles you created, are automatically saved to the originally loaded vizmap.props file in the .cytoscape directory in the user’s home directory.
[!] If you are upgrading from Cytoscape 2.1: If you are upgrading from Cytoscape 2.1, you may want to use your vizmap.props file that is located in your home directory, since this file was used in 2.1 to store visual styles. To do this, you can either specify its location in the command line (edit cytoscape.sh or cytoscape.bat), or copy the file to the .cytoscape directory located in your home directory (on Windows XP, this is the “Documents and Settings” directory, on Linux or Mac this is your home directory, for example, /Users/iavila, or ~/).
Figure: Using the Sample1 Visual Style. Protein-Protein interactions (solid lines) are now distinguishable from Protein-DNA interactions (dashed lines).
Figure: Using the Sample2 Visual Style. Gene expression values are now displayed along a red/green color gradient.
Visual Attributes Associated with Nodes: |
Node Color Node Border Color Node Border Type. The following options are available: ![]() Node Shape. The following options are available: ![]() Node Size: width and height of each node. Node Label: the text label for each node. Node Font: node font and size. |
Visual Attributes Associated with Edges: |
Edge Color Edge Line Type. The following options are available: ![]() Edge Source Arrow. The following options are available: ![]() Edge Target Arrow. The following options are available: ![]() Edge Label: the text label for each edge. Edge Font: edge font and size. |
Global Visual Properties: |
Background Color |
|
Passthrough Mapper |
Discrete Mapper |
Continuous Mapper |
Node Properties |
|
|
|
Node Color |
- |
X |
X |
Node Border Color |
- |
X |
X |
Node Border Type |
- |
X |
o |
Node Shape |
- |
X |
o |
Node Size |
- |
X |
X |
Node Label |
X |
X |
o |
Node Font Family |
- |
X |
o |
Node Font Size |
- |
X |
X |
Edge Properties |
|
|
|
Edge Color |
- |
X |
X |
Edge Line Type |
- |
X |
o |
Edge Source Arrow |
- |
X |
o |
Edge Target Arrow |
- |
X |
o |
Edge Label |
X |
X |
o |
Edge Font Family |
- |
X |
o |
Edge Font Size |
- |
X |
X |
Legend |
|
- |
Mapping is not supported for specified visual property. |
X |
Mapping is fully supported for specified visual property. |
o |
Mapping is partially supported for specified visual property. Support for "continuous to continuous" mapping is not supported. |
Click
the New button, and enter a name for your new visual style when
prompted. Then click the Define button. You will now see the main
Visual Styles Properties dialog box.