This submenu has the following items: Start Shows the control panel of Cluster ONE, which is the main entry With each other) are merged to form larger subgroups to make the results easierĬluster ONE installs itself into the Plugins menu of Cytoscape underĪ submenu named Cluster ONE. Given size or having a density less than a given threshold are thrown away.įinally, redundant cohesive subgroups (i.e. Pair to obtain an initial set of cohesive subgroups. Growth process is repeated either for every vertex or every connected vertex The Cluster ONE paper for the description of the exact procedure. When it is not possible to increase the cohesiveness of the group by addingĪnother external boundary vertex or removing an internal boundary vertex. ![]() Removing a vertex from the group increases its cohesiveness. The cohesiveness of a group as much as possible. Step by step with new vertices so that the newly added vertex always increases Set of vertices that are strongly bound together), one can extend the group This is achievedīy adopting a greedy strategy: starting from a single seed vertex (or a small Mentioned quality measure will be referred to as cohesiveness.Ĭluster ONE essentially looks for groups of high cohesiveness. On, such confidence values will simply be called edge weights and the above You have such confidence values, store them in a numeric edge attribute inĬytoscape and use that attribute to drive the cluster growth process. Should be replaced by the total confidence associated to those edges. We are in its existence), the same guidelines apply, but the number of edges a numeric valueĪssigned to each edge that quantifies how reliable that edge is or how confident Internal edges and only a few boundary edges in other words, the boundary Measure is driven by the fact that a well-defined group should have many The quality of the group can be assessed by the number of internal edgesĭivided by the sum of the number of internal and boundary edges. Marked by a letter are (internal or external) boundary vertices. Thick black edges are internal, thin black edges areīoundary edges, while thin gray dashed edges are completely external. Here, V 0 itself is denoted by a shaded background, which delimits internalĪnd external vertices. Internal boundary vertex, while an external vertex adjacent to at least oneīoundary edge is an external boundary vertex. An internal vertex adjacent to at least one boundary edge is an Internal edge, an edge going between an internal and an external vertex is aīoundary edge, and an edge between two external vertices is an externalĮdge. An edge that is situated between two internal vertices is an Vertices of V 0 areĬalled internal vertices, while vertices not in V 0 are called external Their relationship to a selected group of vertices V 0. Some terminology that classifies vertices and edges of a graph G according to ![]() "growing" dense regions out of small seeds (typically one or two vertices),ĭriven by a quality function called cohesiveness.īefore we move on to the formal definition of cohesiveness, let us introduce For instance, in protein-protein interaction networksĭerived from high-throughput AP-MS experiments, these dense regions usuallyĬorrespond to protein complexes or fractions of them. Of these regions depends on the context (i.e. Regions within the Cytoscape network you are working with. Cluster ONE strives to discover densely connected and possibly overlapping
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