This is the default layout and is always available as part of the Cytoscape core. The grid layout is a simple layout the arranges all of the nodes in a square grid. In addition, many of these layouts include the option to take either node or edge attributes into account. Most of the Cytoscape layouts also partition the graph before performing the layout. panel to change the parameters of the algorithm. All Cytoscape Layouts have the option to operate on only the selected nodes, and all provide a Settings. These layouts are fully integrated with Cytoscape. This algorithm is available by selecting Layout → yFiles → Organic.Ĭytoscape Layouts are those layouts that have been written or integrated by Cytoscape developers. The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph. This algorithm is available by selecting Layout → yFiles → Hierarchical. Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings. The hierarchical layout algorithm is good for representing main direction or "flow" within a network. This algorithm is available by selecting Layout → yFiles → Circular. The circles themselves are arranged in a radial tree layout fashion. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. This algorithm produces layouts that emphasize group and tree structures within a network. The main layout algorithms provided by yFiles are: Due to license restrictions, the detailed parameters for these layouts are not available (there are no yFiles entries in the Settings. YFiles layouts are a set of commercial layouts which are provided courtesy of yWorks. Cytoscape layouts have three different sources, which are reflected in the Layout menu. Most of these features are available from plugins that are packaged with Cytoscape 2.3 and above. The Layout menu has an array of features for organizing the network visually according to one of several algorithms, aligning and rotating groups of nodes, and adjusting the size of the network. Should a network view for the nested network not exist, it will be created. After selecting this the network view of the current node's nested network will be the current network view and have the focus.After being selected the current node will no longer have a nested network associated with it.If the current node already has a nested network it will be replaced. Let's the user select any network in Cytoscape as the current nodes nested network.This menu can change based on the current context. You can hold down the Shift key to select more than one node/edge or you can hold down the left mouse button and drag the mouse to select groups of nodes/edges.Ĭlick the right mouse button on a node/edge to launch a context-sensitive menu with additional information about the node/edge. You can also pan the image by holding down the left mouse button over the blue box in the Network Overview panel in the lower left hand of the Cytoscape desktop.Ĭlick the left mouse button on a node or edge to select that object. You can pan the network image by holding down the middle mouse button and moving the mouse. You can also zoom in/out by holding down the right mouse button and moving the mouse to the right (zoom in) or left (zoom out). Zoom Out to Display all of Current Network.Use the zooming buttons located on the toolbar to zoom in and out of the interaction network shown in the current network display. Panning allows users to move the focus of a screen to different parts of a view.Ĭytoscape provides two mechanisms for zooming: either using mouse gestures or buttons on the toolbar. Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see. ZUIs use two mechanisms for navigation: zooming and panning. Cytoscape uses a Zoomable User Interface for navigating and viewing networks.
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