Settings⦠Opens a dialog where general AutoAnnotate settings can be changed. terms is measured by the Jaccard index of the sets of genes annotated by the. Label Options⦠Opens a dialog where you can select the label algorithm that is used when recalculating labels. Keywords: protein networks, STRING database, Cytoscape, network analysis. Settings Display Creation Parameters⦠Opens a dialog that shows the parameters that were chosen in the Create Annotation Set Dialogįor the current Annotation Set. Set Delimiters Opens a dialog that allows you to add word delimiters. See Removing Words from Labels for more details. Set Excluded Words⦠Opens a dialog that allows you to exclude words from cluster labels. To show the cluster context menu.) Export Clusters to File⦠Creates a TXT file containing the labels of all the clusters. Subset of clusters please select the clusters in the table and right-click Typically used when the WordCloud options or label algorithm changes, or if the contets of Recalculate Labels Recalculates the labels for all of the clusters in the annotation set. Redrawing the annotations can fix this problem.Īnnotations can also be redrawn by clicking the button. Redraw annotations Some versions of Cytoscape have a bug that cause annotations to occasionally beÄrawn in the wrong location. See Cluster-Aware Layoutsįor more details. Layout Clusters The submenu provides access to cluster-aware layout algorithms. When I deleted that other network, the annotations appeared in the annotations panels. ![]() Very similar in functionality to âCollapse Allâ, but runs significantly faster. Im running Cytoscape 3.7.0 with Java on Mac OS 10.14.1. Create Summary Network Generates a new network where each node represents a collapsed cluster in the original network. Consider using the Create Summary Network option instead. Warning: Collapsing all clusters in a large networkĬan be very slow. In the dropdown and delete multiple Annotation Sets at a time. o Often identical to label property of , but not clear that this.Notice how the galFiltered Style maps multiple data and annotation values to. exported by different versions of Cytoscape are annotated with version strings. Manage Annotation Sets⦠Opens a Dialog where you can change the order that Annotation Sets appear Options for deleting selected nodes and edges from the current network. Delete⦠Deletes the current annotation set. Rename Renames the current annotation set. ![]() See Copying Annotations Between Networksįor more details. Copy Annotation Sets from Network⦠Allows annotations to be copied from one network to another. The dialog can also be opened by clicking the button. New Annotation Set⦠Opens the Create Annotation Set dialog.
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