Tutorial
Layouts* Introduction* Install plugins* Import file
* Run
* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Gephi Tutorial
Layouts
Welcome to this advanced tutorial. It will teach you the fine art of network
layout in Gephi: how to use algorithms that place the nodes inside the graphic space.
Gephi version 0.8alpha was used to do this tutorial.

Get Gephi

Last updated June 13th, 2011

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Install layout plugins
We need to install additional plugins.
• Go to the Tools menu and then Plugins.
• In the Available Plugins tab check:- OpenOrdLayout- CircularLayout- GeoLayout- Geometric Transformation- NoverlapLayout• Click on Install. The plugins are installed
and you are asked to reboot Gephi. ClickOK.

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Open Graph File
• Download the file

LesMiserables.gexf• In the menubar, go to File Menu and Open...
• When your file is opened, the report sums up data found and any issues.
- Number of nodes- Number of edges- Type of graph• Click on OK to validate and see the graph.

Graph Format- GEXF- GraphML- Pajek NET
- GDF
- GML

- Tulip TLP- CSV- Netdraw VNA- Compressed ZIP/GZTutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

You should now see a graphWe imported the “Les Miserables” dataset1. This is a coappearance weighted network ofcharacters in the novel “Les Miserables” from Victor Hugo.

Node position is random at first, so you may see a slighty different representation.

1

D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley,
Reading, MA (1993).

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run a layout
Layout algorithms set the graph shape, it is the most essential operation.
• Locate theLayout module, on the left panel.
• Choose “Force Atlas”
You can see the layout properties below, leave default
values.
• Click on

to launch the algorithm.

• You see now the positions of nodes changing in real time.

Layout algorithms

Graphs are usually laid out with “Force-based” algorithms. They follow a simple principle: linked
nodes attract each other and non-linked nodes are pushed apart.

Tutorial
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Control the layout
The purpose of Layout Properties is to let you control the algorithm in order to make areadable representation.
									• Set the “Repulsion strengh” at 10 000 to expand
the graph.
• Type “Enter” to validate the changed value.

										• And nowTips

the algorithm.

Click on the icon
“Center on Graph” on the bottom left of the Visualization panel if you don’t
see the graph anymore.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

You should now see a graph with the layout applied

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Play against the algorithm!
Run the layout again and drag the nodes to stress it.
										• Locate
Dragging action, in the top left of the
Visualization panel.
• Ajust the selection diameter in the panel or byusing the shortcut “Ctrl + Mouse Wheel”.
Increase the “Autostab strength” in the Layout Properties to 100 000, then drag thenodes. The graph becomes less deformed.
• And now

the algorithm.

Tutorial
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Various layouts exist
Gephi implements various layout algorithms. They set the shape of the graph.

OpenOrdForceAtlas 2

Radial Axis

GeoLayout

Airlines sample dataset: http://gephi.org/datasets/airlines-sample.gexf

Tutorial
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So how to choose a layout?
In general, select one according to the feature of the topology you want to highlight:

emphasis
DIVISIONS

emphasis
COMPLEMENTARITIESOpenOrdForceAtlas, Yifan Hu,
Frushterman-Reingold

emphasis
RANKINGemphasis
GEOGRAPHICREPARTITION

Circular, Radial Axis

GeoLayout

Graphic Adjustements- Label Adjust- Noverlap- Expansion- Contraction

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

ForceAtlas layout
Home-brew layout of Gephi, it is made to spatialize Small-World / Scale-free networks.
It is focused on quality (meaning “being useful to explore real data”) to allow a rigorous interpretation of the graph (e.g. in SNA) with the fewest biases possible, and a goodreadability even if it is slow.
Author:
Date:
Kind:
Complexity:
Graph size:Use edge weight:

Mathieu Jacomy
2007
Force-directed
O(N²)
1 to 10 000 nodes
YesTutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run ForceAtlas
the layout by applying the following settings step by step:• Autostab strength = 2 000

Increase to move the nodes slowly.

• Repulsion strength = 1 000

How strongly does each node reject others.

• Attraction strength = 1

How strongly each pair of connected nodes attract each other.

• Gravity = 100

Attract all nodes to the center to avoid dispersion of disconnected components.

• Attraction Distrib. = checked

Push hubs (high number of output links) at the
periphery and put authorities (high number of input links) more central.

And now

the algorithm.

Adjust by Sizes

This option avoids node overlapping, depending on the size of each node.

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Fruchterman-Reingold layout
It simulates the graph as a system of mass particles. The nodes are the mass particles andthe edges are springs between the particles. The algorithms try to minimize the energyof this physical system. It has become a standard but remains very slow.
Author:
Date:
Kind:
Complexity:
Graph size:Use edge weight:

Thomas Fruchterman & Edward Reingold1
1991
Force-directed
O(N²)
1 to 1 000 nodesNo

Fruchterman, T. M. J., & Reingold, E. M. (1991). Graph Drawing by Force-Directed Placement.
Software: Practice and Experience, 21(11).
1Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run Fruchterman-Reingold
the layout by applying the following settings step by step:• Area = 100• Area = 100 000

Graph size area.

• Gravity = 1 000• Gravity = 100

Attract all nodes to the center to avoid dispersionof disconnected components.

And now

the algorithm.

Unstable nodes position!

Sometimes the algorithm does not converge, resulting in an unstable graph. Reduce the “Speed”
setting to gain precision.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Yifan Hu Multilevel layout
It is a very fast algorithm with a good quality on large graphs. It combines a force-directedmodel with a graph coarsening technique (multilevel algorithm) to reduce the complexity. The repulsive forces on one node from a cluster of distant nodes are approximated bya Barnes-Hut calculation, which treats them as one super-node. It stops automatically.
Author:
Date:
Kind:
Complexity:
Graph size:Use edge weight:

Yifan Hu1
2005
Force-directed + multilevelO(N*log(N))
100 to 100 000 nodes
No

Y. F. Hu, Efficient and high quality force-directed graph drawing. The Mathematica Journal, 10(37-71), 2005.
1

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run Yifan Hu Multilevel
Launch the layout by applying the following settings step by step:• Step ratio = 0.99

Ratio used to update the step size. Increase it fora better quality (vs speed).

• Optimal distance = 200

Natural length of the springs. Increase it to placenodes farther apart.

• Theta = 1.0

Approximation for Barnes-Hut calculation. Smaller
values mean more accuracy.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

OpenOrd layout
It expects undirected weighted graphs and aims to better distinguish clusters. It can be
run in parallel to speed up computing, and stops automatically. The algorithm is originally based on Frutcherman-Reingold and works with a fixed number of iterations controlled
via a simulated annealing type schedule (liquid, expansion, cool-down, crunch, andsimmer). Long edges are cut to allow clusters to separate.
Author:
Date:
Kind:
Complexity:
Graph size:Use edge weight:

S. Martin, W. M. Brown, R. Klavans, and K. Boyack1
2010 (VxOrd)
Force-directed + simulated annealing
O(N*log(N))
100 to 1 000 000 nodes
Yes

S. Martin, W. M. Brown, R. Klavans, and K. Boyack, “OpenOrd: An Open-Source Toolbox forLarge Graph Layout,” SPIE Conference on Visualization and Data Analysis (VDA)., 20111

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run OpenOrd
Launch the layout by applying the following settings step by step:• Edge cut = 0.95

• Num iterations = 100• Num iterations = 850• Random seed =-6308261588084905834

Fix node placement

From 0 (standard Frutcherman-Reingold) to 1.
Percentage of the greatest distance between two
nodes in the drawing. A higher cutting means amore clustered result.
Contract the clusters.
Expand the clusters.
Use this value to produce exactly the same shape
as shown before.

Fix the position of a node (or a group of selected nodes) by “Right-click on
it > Settle”. It works for all layouts except Yifan Hu. For OpenOrd, use the“fixed time” setting on the Layout panel to configure the time the fixed
nodes will not move.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run OpenOrd on a large graph
OpenOrd is really helpful on large graphs.
• Import the fileinternet_routers-22july06.gml.zip

This network has 22 963 nodes and 48 436 edges. It is a symmetrized snapshot of thestructure of the Internet at the level of autonomous systems, reconstructed from BGP
tables posted by the University of Oregon Route Views Project. This snapshot was created by Mark Newman from data on July 22, 2006.
If you have a multi-core computer:
Increase the number of threads to execute it in parallel and therefore speed up the execution of the algorithm. It is recommended to set the number of core minus 1 to keepa thread for display.
• Set the “Num Threads” setting or leave default parameters.
• Click on

and wait until it stops.

OpenOrd executes in a finite number of iterations, so you can see the progress on thebottom-right of the screen.

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You should now see a graph with the layout applied

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Go back to the previous workspace
When you imported the second dataset, a new workspace was automatically created.
You are now in the “Workspace 2”. We go back now to the “Workspace 1” where thegraph of Les Miserables still exists.

• Locate the workspace switcher on the bottom-right of the screen.
• You see the name of the current workspace.
• Click on it and select “Workspace 1”. You can either click on the arrows to switch.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

ForceAtlas 2 layout
Improved version of the Force Atlas to handle large networks while keeping a very goodquality. Nodes repulsion is approximated with a Barnes-Hut calculation, which therefore
reduces the algorithm complexity. Replace the “attraction” and “repulsion” forces by a“scaling” parameter.
Author:
Date:
Kind:
Complexity:
Graph size:Use edge weight:

1

Mathieu Jacomy1
2011
Force-directed
O(N*log(N))
1 to 1 000 000 nodes
Yes

http://gephi.org/2011/forceatlas2-the-new-version-of-our-home-brew-layout/

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run ForceAtlas 2
the layout by applying the following settings step by step:• LinLog mode = checked• LinLog mode = uncheckedLinear attraction & logarithmic repulsion (lin-lin
by default), makes clusters tighter.

• Scaling = 100

Increase to make the graph sparser.

• Edge weight influence = 0

From 0 (no influence) to 1 (normal). Set 0 to calculate forces without edge weight.

And now

the algorithm.

Performance

Activate “Approximate Repulsion” on large graphs only, but let’s
try it in this tutorial. Check it, set the “Tolerance” option to
0.04 and run the algorithm to see how nodes are swinging!

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Circular layout
It draws nodes in a circle ordered by ID, a metric (degree, betweenness centrality...) or
by an attribute. Use it to show a distribution of nodes with their links.

Author:
Date:
Kind:
Complexity:
Graph size:

1

Matt Groeninger1
2010
CircularO(N)1 to 1 000 000 nodes

http://gephi.org/plugins/circular-layout/

Tutorial
Layouts* Introduction* Install plugins* Import file
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run Circular Layout• Select the “Circular Layout” in the

Layout panel.

• Set the “Order nodes by” setting to “Degree”.
•

the layout.

• In theRanking panel, choose “Degree” as a rank
parameter.
• Select the diamond icon in the toolbar for size.
• Set a min size at 10 and a max size at 50.
• Click on•

the layout again to avoid node overlap.

to see the distribution of degree.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Radial Axis Layout
It is provided with the Circular Layout plugin. It groups nodes and draws the groups inaxes (or spars) radiating outwards from a central circle. Groups are generated using ametric (degree, betweenness centrality...) or an attribute. Use it to study homophily byshowing distributions of nodes inside groups with their links.
Author:
Date:
Kind:
Complexity:
Graph size:

1

Matt Groeninger1
2011
CircularO(N)1 to 1 000 000 nodes

http://gephi.org/plugins/circular-layout/

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Detect communities
We now want to study the community structure in this network: does it divide naturally
into groups of nodes with dense connections within groups and sparser connections between groups?
In theStatistics panel, click onnear the “Modularity”1 line.

The community detection algorithm created a “Modularity Class” value for each node.
The partition module can use this new data to colorize communities.
• Locate thePartition module on the left panel.

• Click on the “Refresh” button to populate the partition list.

• Select “Modularity Class” in the partition list.
										You can see that 9 communities were found, could be
different for you. A random color has been set for each
community identifier.
							
• Click on
to colorize nodes.
Blondel V, Guillaume J, Lambiotte R, Mech E (2008) Fast unfolding of communities in large networks. J Stat Mech: Theory Exp 2008:P10008. (http://findcommunities.googlepages.com)
1

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Run Radial Axis Layout
Run the layout by applying the following settings step by step:• Group nodes by = “Degree”

Homophily by degree?

• Group nodes by = “Modularity Class”• Order nodes by = “Degree”

Distribution of nodes by degree insideeach community.

• Draw spar/axis as spiral = checked

Better show links inside communities• Draw spar/axis as spiral = unchecked• Ascending order = checked

Better show links between communities

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Geographic map with GeoLayout
The GeoLayout uses latitude/longitude coordinates to set nodes position on the network.
Several projections are available, including Mercator which is used by Google Maps andother online services. The two node attribute columns for coordinates should be in numeric format.
Author:
Date:
Kind:
Complexity:
Graph size:

1

Alexis Jacomy1
2010
Geographic
O(N)1 to 1 000 000 nodes

http://gephi.org/2010/map-geocoded-data-with-gephi/

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Run GeoLayout• Download the file

airlines-sample.gexf and open it.

The network is an undirected graph with 235 nodes and 1297
edges. For each node there are two additional pieces of information - latitude and longitude, both expressed in degrees.

• Go to the• Click on

Layout module and choose “Geo Layout” in the list.

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How to avoid node overlap?
Sometimes the layout is not completely satisfying, as big nodes can overlap smaller. Threedifferent techniques are available to avoid it.
The “Force Atlas” algorithm has an option to take node size into account when applying
a layout.

• Go back to the Workspace 1.
• Choose “Force Atlas” on the

Layout panel.

• Click on “Reset” at the bottom of the panel toreset the layout parameters.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

How to avoid node overlap?
•

the algorithm.

• Check the “Adjust by Sizes” (“Prevent Overlap”
in ForceAtlas 2) option and run it again for a shortmoment.
• Set the “Repulsion Strength” to 1 000.
• Set the “Autostab Strength” to 500.
•

the algorithm.

You can see nodes are not overlapping anymore.

Instability!

This option makes node positions very unstable and disturbs the layout process. Use it at the end of
the layout to refine it.

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Noverlap layout
Use it after any layout to prevent node overlap while keeping the shape of the graph. It
is optimized for big graphs.

• First, run the “YifanHu” layout.
• Select the “Noverlap” algorithm and run it until it stops.
• Reduce the “speed” setting to 0.1 to increase quality.
• Increase the “ratio” at 2 and “margin” at 10 for more
spacing around nodes.

You can see nodes are notoverlapping anymore.

Tutorial
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Label Adjust layout
It works on text size to repulse nodes and therefore makes every label readable. It only
runs on the visible nodes in the Visualization panel.
• Locate the Visualization settings.
• Click on

to activate text display.

• Increase the text size to the maximum.

• Go to the

Layout panel.

• Select the “Label Adjust” algorithm and run it until it stops.

Tutorial
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Geometric transformations
There is no North-South-East-West directions for layouts, and distances are always relative. The same layout on the same graph can produce shapes with different orientations
and scale. Transformation are sometimes useful to compare laid out graphs.
Use the following layouts to do basic transformations on the graph:• “Clockwise Rotate” with angle -90°
• “Counter-Clockwise Rotate” with angle 45°• “Expansion” with scale factor 1.2• “Contraction” with scale factor 0.8

Transformation layout

The plugin “Geometric Transformation” allows to combine rotations, homothetic transformations
and translations at the same time.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Save your project
Saving your project encapsulates all data and results in a single
session file.

Tutorial
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* Choice* ForceAtlas* Fruchterman-Reingold* YifanHu Multilevel* OpenOrd* ForceAtlas 2* Circular Layout* Radial Axis Layout* Geographic map* Node overlapping* Geometric transform* Save* Conclusion

Conclusion
In this tutorial you learned how to use various layouts in Gephi according to the feature
you want to emphasis in the topology and the size of the network, how to avoid node
overlapping and how to do some geometric transformations.

Other layout plugins are available through the Gephi Plugins Center.
Go further:• Gephi Website• Gephi Wiki
• Gephi forum