Styles¶
cy3sbml adds four visual styles to Cytoscape when it starts:
cy3sbml: a light style, the default,cy3sbml-dark: the same mappings on a dark background,cy3sbml-layoutandcy3sbml-dark-layout: the styles of the layout networks (see Layouts), derived fromcy3sbmlandcy3sbml-dark. They have the same mappings, with the node width and height from the columnslayout_widthandlayout_height, and draw the compartments as semi-transparent round rectangles behind the other nodes, with the label at the top.
A style is only added if Cytoscape has no style with this name yet, so a style you changed
and saved in a session is kept. A missing layout style is derived from the current
cy3sbml or cy3sbml-dark style, with your changes of that style.
Every imported network view gets the style named by the property cy3sbml.visualStyle
(default cy3sbml), and the views of the layout networks its layout style (the style
itself if it has no layout style). The property is in the group cy3sbml.props of
Edit → Preferences → Properties... and is saved in the file
~/CytoscapeConfiguration/cy3sbml.props. Set it to cy3sbml-dark to use the dark style for
new imports. To change the style of an existing view, select the style in the Style
panel of Cytoscape.
Mappings¶
The styles map the columns of the network model to visual properties:
| Visual property | Column |
|---|---|
| node label | label |
| node shape, size, label font and label position | sbml type |
| node fill color | sbml type ext (reversible and irreversible reactions have different colors) |
| node border color | compartmentCode (one color per compartment, for up to 8 compartments) |
| node border line type | cofactorClone (dashed for the clones of split cofactor nodes) |
| edge line type and target arrow shape | interaction type |
| edge color, source arrow shape and arrow colors | shared interaction (activators and inhibitors have their own colors) |
The node label is a passthrough mapping, all other mappings are discrete mappings; the layout styles add passthrough mappings for the node width and height. You can change the mappings in the Style panel like in any other style, and save the result in your session.