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CoPAP Frequently asked questions




  1. Visualizing a network using Cytoscape
  2. Clustering CoPAP results using Cytoscape clustering plugins



  1. Visualizing a network using Cytoscape

    From the CoPAP results page, press the "Open the network using Cytoscape" link and download the jnlp file. Opening the jnlp file will load the Cytoscape java applet and the co-evolutionary network inferred by CoPAP.
    Here are introductory Cytoscape tutorials you might find useful:

    For the full Cytoscape user-manual have a look here.

  2. Clustering CoPAP results using Cytoscape clustering plugins

    From the CoPAP results page, press the "Open the network using Cytoscape" link and download the jnlp file.

    Opening the jnlp file will load the Cytoscape java applet and the co-evolutionary network inferred by CoPAP. Several Cytoscape plugins are pre-loaded with Cytoscape allowing the analysis of the network.
    Here we provide a basic tutorial to cluster the CoPAP network into modules with the TransClust plugin. For more comprehensive tutorials about clustering and the different parameters for each algorithm have a look at clusterMaker tutorial or TransClust tutorial.

    To cluster the CoPAP network into modules with the TransClust plugin:
    1. Under plugins menu select "cluster" and "Transitivity Clustering" (Plugins->Cluster->Transitivity Clustering)
    2. Select minLog_CoEvolve on the "Array sources" menu (see Figure 1)
    3. Press "Create clusters"
    4. To open a new view with the created clusters, press the "Visualize cluster" button

        FIGURE 1 Transitivity Clustering Settings.



    5. Dragging the mouse while the left button is pressed allows you to select a cluster of nodes for further investigation. If the CoPAP run was provided with characters annotation data, such a selection will allow you to see:
      1. The annotation of each node in the selected cluster (on the node attribute browser tab, located on the lower part of the screen)
      2. The annotation of each edge in the selected cluster (on the edge attribute browser tab)

    6. You can export the clusters annotation to a file by
      1. selecting all nodes (using ctrl+A),
      2. Press on the button and check the "0_TransClust_Cluster" box
      3. Right mouse click on the table area and select Export->Entire table.
      4. The produced file is a tab delimited file which can be opened in any text-editor or, for example, Microsoft Excel. Each cluster has a unique ID under the "0_TransClust_cluster" column.

    7. Additional network analysis can be performed using the "Network Analysis" plugin: select Network analysis under the Plugins menu and then select the Analyze Network option ("Plugins"-> "Network Analysis"-> "Analyze Network").

      In the opened window select the option to treat the network as undirected. The analysis includes "Clustering coefficient", "Characteristic path length" and many additional attributes for network properties (see Figure 2).

        FIGURE 2 Network Analysis.



    Similar procedures can also be applied using other clustering methods available on the Plugina->Cluster menu.