![]() This will tell Cytoscape to generateĪ label for the group node that aggregates the labels of the nodes in the cluster. When switching between Annotation Sets all collapsed clusters are automatically expanded.Ĭlusters can be collapsed or expanded from the Annotation Set Menu or the Cluster Table Context Menu.īefore collapsing clusters make sure that node aggregation is enabled. It is not recommend to manually collapse or expand clusters using the Groups menu as this may confuse AutoAnnotate. When a cluster is expanded the group node is expanded and then deleted. The label shown for a collapsed cluster is generatedīy Cytoscape and depends on the Group Preferences (explained below). Figure 6-16 shows a complete explanation of the. The annotation for a cluster is not shown when the cluster is collapsed. Cytoscape does have some text and drawing annotation tools available via the right-click context menu. The collapsed group nodes and the meta-edges provide a summary of the network. When the cluster is collapsed Cytoscape will create “meta-edges” between the group node any other nodes it isĬonnected to. When AutoAnnotate collapses a cluster it first creates a group node that contains all the nodes in the cluster and then the group A group node is a compound node that contains other nodes. The Cytoscape “group nodes” feature is used to collapse and expand clusters. See the section below this one for more details. Consider using the “Generate Summary Network” option insteadīecause it runs significantly faster. Warning: As of Cytoscape 3.4 this function can be very slow, depending on the Settings… Opens the AutoAnnotate settings dialog.ĪutoAnnotate can summarize a network by collapsing some or all of the clusters automatically. To show the cluster context menu.) Label Options Opens a dialog where you can select the label algorithm that is used when recalculating labels. Subset of clusters please select the clusters in the table and right-click Typically used when the WordCloud options or label algorithm changes. Recalculate Labels Recalculates the labels for all of the clusters in the annotation set. Redrawing the annotations can fix this problem. Redraw annotations Older versions of Cytoscape have a bug that cause annotations to occasionally beĭrawn in the wrong location. Layout Clusters Runs a layout algorithm that will layout each cluster separately using the perfuse Very similar in functionality to “Collapse All”, but runs significantly faster. Expand all Expands all the clusters Create Summary Network Generates a new network where each node represents a collapsed cluster in the original network. Warning: Collapsing all clusters in a large network can be very slow.Ĭonsider using the “Create Summary Network” option instead. In the dropdown and delete multiple Annotation Sets at a time. Rename Renames the current annotation set Delete… Deletes the current annotation set Manage Annotation Sets… Opens a Dialog where you can change the order that Annotation Sets appear New Annotation Set… Shows the Create Annotation Set dialog. To edit the label for any node, select Customize/Edit from the right-click context menu, and edit the text in the ensuing dialog.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |