Groups by Partition Plugin for Gephi: “Each node is the aggregation of a group of nodes”

Dr. Verónica Espinoza, 2023. Twitter @Verukita1 LinkedIn: Dra. Verónica Espinoza

Image by the author

What can i do with the Groups by Partition plugin for Gephi?

This plugin creates a graph where each node is the aggregation of a group of nodes (of the previous workspace) using the colors given to the nodes [1].

What will we review in this story?

In this story I will share how I have used the Groups By Partition plugin [1] for Gephi [2,3] and the steps I take to generate this type of network.

First, download the Groups By Partition plugin here

Step 1.
Upload your file of choice to the Gephi tool and work your network as usual. In this example I uploaded a Wikipedia file whose data was extracted from the NodeXL tool. The query was “Neuroscience”, level 2.0.

In Gephi, I worked this file with the following parameters:

1. -Statistics > Community Detection > Modularity.
2. Apparance > Nodes> Partition color >Modularity Class.
3. Apparance > Nodes > Ranking size > Degree.
4. Apparance > Nodes > Ranking label > Degree.
5. Layout > Force Atlas 2 > Stronger Gravity > Scaling 3.0.

Figure 1a. Network obtained by applying the described parameters.

Now, download the network as a “original network" before applying the Groups by partition plugin. In this example, I downloaded the netwwork in PNG format, as shown below.

Figure 1b. Network exported in PNG format.

Step 2. Open the plugin Groups by Partition as shown: Tools > Generate groups by partition.

Figure 2. The path to open the plugin is shown.

Step 3. Click on “Create” button to create a new worksplace.

Figure 3. “Create button” to create a new worksplace.

Step 4. As you can see, each node has been added to a group of nodes.

Figure 4. Aggregation of a group of nodes.

Step 5. Now, you can apply another layout so that the groups are better distributed, it works well for me to apply the Fruchterman Reingold layout and increase the value of the area parameter, as you can see in the following image. You can also adjust again the size of the nodes and labels in the appearance section until you are satisfied with the results.

Other parameters that I recommend you adjust to have a better visualization of your network are:

· Noverlap.

· Label Adjust.

· Expansion.

*These parameters are found in the Layout section.

Figure 5. Adjustment of new parameters for a better visualization of the network.

Step 6. View your network in the preview section and make the last adjustments if you think it is necessary.

Figure 6. Re-adjusting the parameters if necessary.

Step 7. When you are happy with the results, export your network in the format of your choice (SVG/PDF/PNG).

Figure 7. Results of the network using the Groups by Partition plugin.

Final comments

In this story I have shared my experience on how to use the Groups by partition plugin for Gephi, but you can “play” with other parameters or apply other layouts until you are satisfied with your results.

I think this plugin can be very useful when we have networks with a large number of nodes and edges. By applying this plugin, we will have a visualization that will help us highlight which are the most important groups in our study.

I hope this interesting plugin is useful for you and that you can apply it in your research projects.

👍Thanks for reading this story.

😃My Twitter

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Do you want to learn more about Gephi?

I share other tutorials that I have written about Gephi:

1. How to publish your Gephi network to the web.
2. Link Prediction Plugin for Gephi.
3. Position Ranking Plugin for Gephi,
4. How to visualize a Spotify Network in Gephi in just a few steps!
5. How to use Network Splitter 3D plugin for Gephi
6. How to use Word Cloud plugin for Gephi
7. Meet the Gephi color palette and make beautiful visualizations
8. What is Gephi? Meet this useful network analysis tool.

Resources

🌐 Group for Partition plugin

📄 Source code

📥Download Gephi here

🎓My Gephi story on Medium

REFERENCES

1. Groups By Partition Plugin [Internet]. [cited 2023 Feb 6]. Available from: https://gephi.org/plugins/#/plugin/group-partition-gephi-plugin
2. Gephi — The Open Graph Viz Platform [Internet]. [cited 2023 Jan 31]. Available from: https://gephi.org/
3. Bastian M., Heymann S., Jacomy M. (2009). Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media