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Gephi: Visualizing

This guide collects resources and tutorials for using Gephi, a network analysis and visualization program.

Outline

Tutorial Data

Tutorial Slides

Tutorial Handout

Tutorial Video

Visualizing

Load data

  • Load "nodes" table
    • Create a new project
    • Click on "Data Laboratory"
    • Click on "Import Spreadsheet"
    • Use separator "tab"
    • As table "Nodes table"
    • Click "Next"
    • Change agerank format to "Integer"
    • Change latitude and longitude formats to "Float"
    • Note: For nodes tables, you should have an "Id" column that specifies the name of the node.  The values in this column should match up with the names of nodes in the "edges" table.
  • Load "edges" table
    • Click on "Import Spreadsheet"
    • Use separator "tab"
    • As table "Edges table"
    • Default settings okay
    • Note: For edges tables, column labels are important.  Gephi expects "Source" and "Target," at least.  Gephi will create a "directed" network by default.  If you want an "undirected" network, you need a column named "Type" with "Undirected" in the cells.

Layout

  • The "layout" is how the software arranges the nodes and (consequently) the edges in the network; different layouts prioritize different properties of the networks 
  • Choose a layout from the drop-down list (e.g., ForceAtlas 2)
  • Optional: adjust parameters for the layout algorithm
  • Click the "Run" button
  • Continue to refine the layout until you are happy with the results

Color

  • The sample network has a "partition" (categorical) node variable called "State"
  • Click on "Partition"
  • Click on "Nodes"
  • Choose "State" from the drop down
  • Click the "Apply" button

Filter

  • Click the "Filters" tab on the right
  • Expand the "Typology" folder
  • Double-click the "Giant Component" filter
  • Click the "Filter" button
  • Note: Nested filters can be a bit tricky.  You might think in order for Gephi to apply one filter before another, the first filter should be at the top, higher in the list.  You actually want it the other way, though; Gephi wants the first filter at the innermost level (or on the bottom of the list).

Size

  • Resize nodes uniformly
    • Click on the selection box icon on the left vertical toolbar
    • Draw a box around all nodes to select them all
    • Click on the diamond icon on the left vertical toolbar
    • Click on a node, then drag the mouse up and down to increase and decrease the size
  • Resize nodes according to a numerical variable
    • Click on the "Ranking" tab
    • Click on "Nodes"
    • Select a variable (e.g., Degree) from the drop down
      n.b.: Degree is calculated automatically by Gephi for each node.  It is the number of edges connected to each node.
    • Choose a minimum and maximum size to be mapped to the range of the variable
    • Click the "Apply" button

Animate

  • Gephi has a "Timeline" function that can be used to animate a network over some kind of time-based variable
  • In the Data Laboratory, click "Merge columns"
  • Move the starting time column (here, "date") into the "Columns to merge:" box.  If you also have an ending time column, also add that.
  • Select "Create time interval" from the drop down and click "Ok"
  • Specify the start and end time columns on the next screen, deselecting if necessary
  • If the time columns include basic numbers (like the order of appearance), select "Parse numbers" and specify optional default times
  • If the time columns have some sort of date format, use "Parse dates" and specify the date format. It’s very picky – do MM/dd/yy if there are only two year digits!
  • In the "Overview" pane, click "Enable timeline" at the bottom
  • If the timeline looks strange - has many large numbers instead of dates - you may need to adjust the display settings.  Click on the settings gear at the bottom-left corner of the timeline and select "Set time format...".  Change the format to Date.