## page was renamed from HyperEdgeEditor
A Cytoscape Edge typically connects two Nodes, which we commonly refer to as Source and Target Nodes. While this is sufficient for most cases, there are cases, such as for biochemical reactions, where you may want to have Edges that connect more than two Nodes. The Hyper''''''Edge''''''Editor plugin for Cytoscape enables you to do this.

The figure below shows an example of a biochemical reaction, where an Edge represents a ''reaction'' that may have multiple ''substrates'', ''products'', and ''mediators''.

{{attachment:biochemcial_reaction_eg.png}}

Here L-glutamine and 2-oxoglutarate are ''substrates'' for the ''reaction'', the ''catalyst'' glutamate substrate is a ''mediator'' for the ''reaction'', 2 L-glutamate is a ''product'' of the ''reaction'', the ''co-factor'' NADPH is a ''substrate'' for the ''reaction'', and the ''co-factor'' NADP is a ''product'' of the ''reaction''.

There may also be cases in which you may want to connect one edge with another edge, for example to represent the activity of a ''molecular species'' that modulates the action of a ''catalyst''. This is illustrated in the figure below

{{attachment:edge_connect_edge.png}}

where ''molecular species'' S_643 inhibits the action of ''catalyst'' M_643.

If you look closely at these two figures, you will see some small squares at the intersections of the edges. In Cytoscape, we refer to this small square as a !ConnectorNode. We also refer to the collection of edges and !ConnectorNode as a !HyperEdge.

To edit biochemical reactions in this manner, you need to first install the Hyper''''''Edge''''''Editor plugin for Cytoscape. The Hyper''''''Edge''''''Editor is an extension of the Cytoscape''''''Editor and includes all of its basic functionality.  Then, using Cytoscape's Editor and the ''Bio''''''Chemical''''''Reaction'' visual style, you can build and modify ''reactions'' by dragging and dropping shapes from the editor palette onto the main network view window. You can add ''products'', ''substrates'', and ''mediators'', to a ''reaction''.

The figure below shows the Editor palette for the ''Bio''''''Chemical''''''Reaction'' visual style and the result of dragging/dropping the ''Add''''''Reaction'' shape from the palette onto the canvas.

{{attachment:hyperEdgeEditor.png}}

The ''Add''''''Reaction'' palette shape serves as a template that enables you to add a connected set of nodes and edges to a network. You can change the names of the ''substrates'', ''products'', and ''mediators'' by editing them in Cytoscape's Attribute Browser.

You can connect additional ''products'', ''substrates'', and ''products'' to a ''reaction'' by dragging their associated shapes from the palette and dropping them on the ''reaction's'' !ConnectorNode. An example of a ''reaction'' with two ''products'' is shown in the figure below.

{{attachment:hyperedge_two_products.png}}

An example of a ''reaction'' with two ''products'' and two ''substrates'' is shown in the figure below.

{{attachment:hyperedge_two_products_two_substrates.png}}

You can connect a conventional Cytoscape node to a ''reaction'' by creating an edge from the conventional Cytoscape node to a !ConnectorNode (via drag/dropping an edge from the editor palette onto the node). Conversely, you can connect a ''reaction'' to a conventional Cytoscape node by creating an edge from the !ConnectorNode to the conventional Cytoscape node (via drag/dropping an edge from the editor palette onto the !ConnectorNode).

You can also create a !HyperEdge from a Node to a regular edge by by first dropping an edge palette item onto a Node (source) and then dropping again (with the rubberband edge) on another Edge (target). If the source node is a regular node and the target is a regular edge--the target edge is removed and a !HyperEdge is created that connects source node, target edge's source and target edge's target. This was shown in the example on catalyst action at the top of this section (shown again below).

{{attachment:edge_connect_edge.png}}

Hyper''''''Edges can also be connected to each other and chained together. For example, if you drop an edge palette item onto a Connector''''''Node (source), then drop the rubberband edge on an Edge (target), then a !HyperEdge-!HyperEdge connection will be created (need example). Also, if you drop an edge palette item onto a regular Node (source), then drop the rubberband onto a !HyperEdge edge (target), then a !HyperEdge-!HyperEdge connection will be created (need example).

The popup menu presented when right-clicking on a !ConnectorNode will bring up an additional !HyperEdgeEditor submenu that allows selection and deletion of !HyperEdges. Since !HyperEdges must have a minimum of 2 edges, deleting a !HyperEdge may lead to a cascade of deletions if the deleted !HyperEdge has shared edges with other !HyperEdges.

Deletion of Nodes and Edges using will update the corresponding !HyperEdges. 

!HyperEdges can be saved and exported along with any Cytoscape Network, with attributes as XGMML. This assumes the !HyperEdge plugin is loaded before you open or import your sessions and networks.

The following two figures show examples of BiochemicalReactions that you can build up using Cytoscape's editor. Once the !HyperEdgeEditor plugin is loaded, you can perform File->Import->!HyperEdge Sample Networks. There are two sample networks--Krebs Cycle and Glycolysis Reaction.

The first figure below illustrates Glycolosis Reaction. Note the use of shared edges and multiple connections to the same Node within a !HyperEdge.

{{attachment:glycolosis.png}}

The second example below uses a Circle Graph Layout to illustrate the Krebs Cycle.

{{attachment:krebs_cycle2.png}}

=== A Closer Look ===
The !HyperEdgeEditor uses an underlying !HyperEdge plugin that contains a [[HyperEdgeAPI]] for use by plugin writers to create and manipuate HyperEdges.

As was stated earlier, a ''Biochemical''''''Reaction'' is composed of a set of ''substrates'', ''products'', and ''mediators'', and a Hyper''''''Edge that connects them. Here are some basic definitions, plus some rules and constraints for working with Hyper''''''Edges:

A !HyperEdge is an Edge that connects two or more Nodes. A !HyperEdge consists of a set of Edges and a special Node referred to as a !ConnectorNode. The !ConnectorNode is a generated Node that serves as one endpoint for all Edges contained by a !HyperEdge.

Some definitions for !HyperEdges are:

 1. !HyperEdges are mutable. You can add and remove nodes and edges to and from them.
 1. A !HyperEdge may have more than one !CyNode with the same !CyEdge interaction type.
 1. A !HyperEdge may have more than one !CyEdge to the same !CyNode.
 1. A !HyperEdge has exactly one !ConnectorNode.
 1. A !HyperEdge !ConnectorNode may be used as a regular !CyNode within another !HyperEdge.
 1. A !HyperEdge is associated with one or more !CyNetworks.
 1. The only shared !CyEdges in a !HyperEdge are those connecting two !ConnectorNodes (!HyperEdges) that must exist in the same !CyNetwork.
 1. If !HyperEdge A connects to !HyperEdge B via a shared edge, both A and B can only exist in one (and the same) !CyNetwork.
 1. A regular Cytoscape Edge may directly connect to a !HyperEdge !ConnectorNode, but it will not be considered part of the !HyperEdge.
 1. !HyperEdges are shared, in that any change to a !HyperEdge existing in more than one !CyNetwork is reflected in all !CyNetworks to which the !HyperEdge belongs.