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Learning Outcomes
  • Learn how to launch the Network Explorer app in different modes.
  • Understand how to input network data from various sources.
  • Customize node options with additional metadata.
  • Explore network layout and centrality options.
  • Utilize node selection features effectively.

Network Explorer Tutorial

Launching Network Explorer

Launching in Stand-alone Mode

To launch the Network Explorer app in standalone mode, follow these steps:

  1. Click on Apps in Foundry's top banner.
  2. Navigate to the Shared Apps tab.
  3. Search for Network Explorer or locate it in the table.
  4. Click Launch.

Launching from the Report Tab

You can launch the Network Explorer app with pre-loaded data after completing a Foundry run by doing the following:

  1. Open the completed run and select the Report tab.
  2. Choose any file with an .Rmd extension.
  3. Click Launch in the Network Explorer box.

Network Input

You can source network information from various locations:

STRING

To extract all annotated protein-protein interactions for a specified protein from the STRING database:

  1. Select stringDB as the input source.
  2. Provide the gene or protein of interest.

Toggle the "Include Secondary Neighbors" option to add interactions that are two degrees away from the specified protein.

User Defined

Users can upload a network of interactions using a tab-separated input file containing edges. The minimal file should have at least two columns:

  1. source
  2. target

Ensure the uploaded file contains columns named exactly "source" and "target".

Node Options

You can upload additional metadata for nodes in the Metadata section to customize node appearance. If launched from the Report tab, corresponding metadata will be pre-loaded when possible. You can still upload additional metadata by setting the Metadata Source to 'Manual':

  • The minimal metadata file must include a column titled exactly "gene," where the values correspond to the IDs of the nodes.
  • Control node color and size according to metadata and calculated values (e.g., node centrality) by selecting an appropriate column. Only columns with numeric data will be available.

Layout

To change the network layout, select the desired option from the drop-down menu in the layout panel.

Centrality

Centrality will be calculated for every node based on the selected centrality algorithm. You can choose from the following algorithms using the drop-down in the centrality panel:

Please note that additional parameters may be required depending on the chosen algorithm.

Zoom

You can automatically zoom the network to fit all nodes or only the currently selected nodes using the zoom panel.

Node Selection

Select nodes by clicking on their corresponding circles on the graph. Holding Shift or Ctrl allows for the selection of multiple nodes. Alternatively, you can select specific nodes in the selection box and then click the "Select" button.

To unselect nodes, click on a selected node, or click the 'Unselect All' button to deselect all nodes at once. The "Get Neighboring Nodes" button will select all nodes adjacent to the currently selected node(s).

Node Metadata

Access node data by selecting the "Node Properties" tab above the graph. This section displays internally calculated values and any uploaded metadata.