cytoscape_usage – Loading Results with Cytoscape

For this visualization, we will use the real edge table (real_edge_table.txt) and real node file (real_node_table).

The following are the directions to use once Cytoscape is installed and open:

1. File -> Import -> Network from Table

   1. Select: “real_edge_table.txt” file
   2. Click: Show Text File Import Options
   3. Click: Transfer first line as attribute names
   4. Select: Source Interaction = Column 1
   5. Select: Target Interaction = Column 2
   6. Click the headers for all other columns to import them (they will turn blue: note, might need to clicked more than once)

• As a result, you should get successful import message.

2. File -> Import -> Attribute from Table

   1. Select: “real_node_table.txt” file
   2. Click: Show Text File Import Options
   3. Click: Transfer first line as attribute name
   4. Click: Import

• As a result, you should get successful import message.

3. Click: VizMapper

• The user can set different properties, e.g. node color, by double-clicking.

  • Select: as “Discrete Mapper”
  • Select: Attribute to color by

• The user can also explore layouts by using Layout from the menu bar.

Note: some layouts will take a very long time to run on large datasets.