This directory contains plugins which are loaded when Cytoscape starts up. Adding plugin .jar files to this directory will cause them to be automatically loaded whenever Cytoscape is run. The current version of Cytoscape comes preconfigured with the following plugin files in this directory: HierarchicalLayout.jar ---------------------- This plugin adds a choice to the Layout menu labelled "Apply Hierarchical Layout". Choosing this item causes the graph nodes to be repositioned in an approximately optimal configuration for a tree-like directed graph. As much as possible, nodes will be positioned in layers so as to minimize the number of edges which point upwards. If the graph is acyclic, no edges should point upwards. Also, connected components are separated, and some effort is made to reduce the number of edge crossings (the method seeks to acheive fair quality with minimal runtime complexity). This method can also be applied to a selected subset of nodes (>1), which will be layed out separately from the rest of the graph. MCODE.jar --------- This plugin adds a choice to the Plugins menu labelled "MCODE". Through this menu you can access the MCODE analysis routines ("Molecular Complex Detection"), that detect densely connected regions in large networks. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. SigAttributes.jar ----------------- This plugin add a choice to the Plugins menu labelled "Find Enriched Attributes". This item allows you to scan for significant attributes loaded onto the network. The scan can be performed by Attribute or by Annotation, and is based on a group of selected nodes. control.jar ----------- This plugin add a choice to the Layout menu labelled "Align". This item will display a toolbar which allow you to align and distribute selected nodes relative to each other (Align/Distribute horizontal left/center/right, Align/Distribute vertical top/center/bottom) diff.jar -------- This plugin add a choice to the Data menu labelled "Diff". In order for this plugin to function properly, the plugin in "filter.jar" must also be loaded. The "Diff" menu item allows the user to compare two networks, and will display differences found. Filters that have been created can also be applied during the comparison. filter.jar ---------- This plugin adds a new menu named "Filters", a toolbar button to access the "Use Filters" function, and a menu item labelled "Attribute Browser if passed Filter" to the Data menu. Through these controls, the user can define a set of conditions which define a subset of the graph. These sets of conditions can be used to select, browse, or compare subsets of the currently viewed network. jgraphLayout.jar ---------------- This plugin adds a new choice to the Layout menu labelled "JGraph". Through this submenu, the user can apply several layout algorithms to the currently viewed network. Circle (all nodes in a single circle), Radial (nodes in concentric circles), Spring (embedded spring energy minimization), and Sugiyama (layered hierarchical) are possible choices. layout.jar ---------- This plugin adds several new layout choices to the Layout menu: ISOM (spring embedded), Radial (polar coordinates), Circle (all nodes in a single circle), Spring (local spring embedded optimization) yLayouts.jar ------------ This plugin add a new choice to the Layout menu labelled "yFiles". Through this submenu, the user can apply several layout algorithms and view transforms including Circular, Organic, Scale, Hierarchic, Random, Tree, MirrorX, MirrorY, Rotate, and Orthogonal. yeast-context.jar ----------------- This plugin adds a context sensitive menu to Cytoscape that enables links to Saccharomyces cerevisiae web resources. It can be accessed by right-clicking on any node, but is only relevant for budding yeast networks.