Graphics Reference
In-Depth Information
Figure 7-19:
This is the main window of Cytoscape.
You can find graph statistics under the Tools menu and apply them to any
selected subset of the graph.
Layouts in Cytoscape are not as interactive as in Gephi. You pick a layout
from the Layout menu, and the new graph layout appears. Adjusting a
layout requires trial and error. Select Layout
⇒
Settings, adjust a property,
select Layout again, and repeat until you are satisfied with the results. One
alternative is that you can generate the layout in another program (for
example, Gephi or yEd), export it as GraphML, and then import it into
Cytoscape.
Tip
If you already have x and y positions for nodes (for example, latitude
and longitude, or positions generated in other software), you won't find
a layout for these. Instead, Cytoscape provides visual attributes for
node x and node y positions.
Although Cytoscape does not have layouts that tweak node positions in the
current version, it does make it easy to click and drag to move nodes or
groups of nodes or apply layouts to a selected subset of the graph.
Selection and filtering work together. You can select parts of the graph via
click, click-and-drag, the Selection menu, or filters. You can then act upon
