Visualization of data in HoPaCI
- Pop-up windows show the information that is basis of the interactions
- Hovering over arrows/edges opens an info box with detailed information about the underlying interactions.
- Clicking on an arrow/edge results in opening new windows with the complete entry information, one for each entry.
- The thickness of an edge correlates with the number of interactions found for the same subject, object and interaction symbol.
- Moving objects/nodes
In order to move nodes (proteins, chemical compounds etc.) one first has to click on the yellow icon below the "Help" link.
Secondly, the user has to click on the respective node which in turn appears in darker colour. In this state, the node can be moved by using the left mouse button.
- Extending the graph for items of interest
Double clicking on an object (node) launches a new search extending the current information for all interactions that are associated with the respective node.
- Zooming and moving of the graph
For zooming the graph either the mouse wheel or the zoom function on the upper left of the graph can be used.
For moving the graph the left mouse button has to be hold down and the mouse to be dragged in the appropriate direction.
- Hide/show transitive interactions
Per default the graph not only shows the interactions of the search results but also interactions between the objects,
i.e. if a search finds a-b and a-c, a relation between b and c will also be shown, even if it is not found by your search.
If you do not want to see these relations click on the "Hide transitive relations" button on the lower left of the graph. To open them again click a second time on the same button.
- Graph download
Diagrams can be downloaded as SBML, graphML or jpg files by clicking on the respective buttons on the lower left of the window.
SBML: SBML files can be processed by numerous software tools (see SBML Software Guide). Instructive layout styles for Cytoscape users are e.g.
yFiles organic, yFiles orthogonal, Cytoscape Force-Directed Layout, Cytoscape Spring Embedded and Cytoscape Edge-Weighted Force-Directed.
GraphML: Users that want to edit the graph should use the graphML format. The file can be opened and edited with the freely available yED software (http://www.yworks.com/en/products_yed_about.html)