Gephi FAQ

Students in my Kellogg MBA and EMBA Social Dynamics and Networks classes do a lot of work using the network analysis and visualization software package Gephi. As with any unfamiliar software, there are often a few bumps along the road. I thought it would be helpful to compile a Gephi FAQ, so I scanned through my old emails looking for Gephi questions and have posted some of the most common ones here along with their answers.

Q1. How can I filter the network so that I only see the largest connected component?

A. In the statistics window, click the run button next to connected components. Then, switch to the filters window. Select the Attributes folder, then the Partition folder. Then drag the "Component ID (Node)" filter down to the Queries window where it says "Drag filter here". You can select which component(s) you want to see by clicking on the check boxes next to the component numbers where it says "Partition (Component ID) Settings" You can see what fraction of the nodes belong to each component as a percentage next to each component number, so if you only want to see the largest connected component, chose the one with the highest percentage. Then click Filter.

Q2. When I try to export my graph as a pdf, Gephi clips the node labels so that I can't see all of them. How do I fix this?

A. There is no good way to fix this, but there is a work around. When Gephi exports the image, it only pays attention to nodes and links, not the labels, when it decides where to clip the image. To make sure you get the full image, you can add some nodes around the edges of where you want to clip the image. To do this, there is a tool on the left side of the overview window that looks like a pencil (the top one of the two pencils). Just click on the screen with this tool where you want the new node to appear. Put one node on the left, right, top and bottom at the boundary of where you want the image to be clipped. Then, so these nodes don't actually show up, you can resize them so that they're so small that they can't be seen. To do this, select the sizing tool, which looks like a little diamond on the left side of the overview window. Then click on the node that you want to reize and drag the mouse down to make the node smaller. This should fix the problem.

Q3. I imported a graphml data file and I'm trying to use eignevector centrality (PageRank, HITS, …) to identify important nodes, but when I try to run the eigenvector centrality calculation from the Statistics window nothing happens. How do I fix this?

A. The problem is that the graphml file that you imported already has (empty) columns corresponding to the measures that you want to calculate and Gephi won't overwrite them. To fix this, you first have to delete those columns. Go into the data laboratory tab and delete any of the columns that have to do with measures of centrality like eigenvector centrality, closeness centrality, betweeness centrality, page rank, anything that looks like that.  Once you have done that go back to the overview window and then run the calculation that you want under the statistics tab. If the little window pops up with the graphs, then everything is working, if it doesn't then you need to go back to the data laboratory and delete some more columns.

Q4. I imported a node attribute that I want to use to resize my nodes, but it isn't showing up under the ranking tab. How do I fix this?

A. The most likely problem is that the node attribute is identified as the wrong type of data — probably a String, when it needs to be a numeric type such as BigInteger. The easiest way to fix this is to click Duplicate column in the data laboratory and then be sure to select a numeric type (e.g. BigInteger or BigDecimal) for the duplicated column. Once you're done you can delete the original node attribute column. The duplicated numeric column should now be accessible in the rankings window.

Q5. I'm trying to import an adjacency matrix that I have in a csv file, but I keep getting the  java runtime error “java.lang.RuntimeException: java.lang.NullPointerException” What do I do?

A. For some reason, when importing an adjacency matrix Gephi expects a csv file with semicolon separators, not commas. Just open your csv file using a simple text editor like NotePad or TextEdit and then use the Find/replace command to change all of the commas to semicolons.

Q6. I have a network in which there are different types of nodes (e.g. doctors and patients) and I would like to color the different types using different colors. How do I do this?

A. You need to import a new node attribute that gives the type for each node. To add a node attribute, create a spreadsheet with one column labeled Id that contains a list of all of the names of the nodes in your network. Be sure these are the same names that appear under the ID column in the Data Laboratory in Gephi. Then add additional columns to the spreadsheet that give the node attributes for each node. For example, you might have a column called "type" with entries like "doctor" or "patient" that tells whether the corresponding node is a doctor or a patient. Once you have created your spreadsheet, export it as a csv. Now, go back to Gephi with your existing network file open. Under Data Laboratory, select Import Spreadsheet, and choose Nodes Table. Make sure that the button “Force Nodes to be Created as New Ones” is not checked. and import the spreadsheet. This should add a new column to the nodes table in the data laboratory. Then, using the partition tab, you can color the nodes according to this attribute.

Q7. I'm trying to import an adjacency matrix from a csv file, but I'm getting the error "java.lang.RuntimeException: java.lang.Exception: Inconsistent number of matrix lines compared to the number of labels” What do I do?

A. One thing to try is removing any extra spaces from your csv file. Sometimes these trip up the import. Open the csv file using a simple text editor like NotePad or TextEdit, and then use find/replace to remove any spaces. Save the adjacency matrix and then try importing it again.

Q8. I'm trying to import an edge list, but I just get a bunch of nodes with no edges. What's going wrong?

A. Make sure that when you're importing the edge list from the data laboratory that you select  "Edges Table" in the drop down menu and not "Nodes Table." Otherwise it just thinks your bringing in a list of nodes.

Q9. I want to add labels to my network, but when I click the little black T, no labels show up (or the label isn't what I want it to be). How do I get the (right) labels?

A. You need to feel Gephi which column you want it to use for the labels. By default, Gephi uses the data in the column "Labels." To change which column is used, from the over view screen, click the small triangle in the lower right hand corner of the Graph window, which will reveal an extra settings pane. Then choose the Labels tab. On the far right hand side of this window, click "Configure…" then put a check mark next to any of the attributes that you would like to show up as labels. Alternatively, in the Data Laboratory, you can just copy the column that you want to use as labels in to the labels column.

Free online complex systems course by Scott Page!

Yesterday I talked with Scott E. Page from the University of Michigan and Santa Fe Institute and he pointed me to an amazing opportunity. He will be teaching a free online course on complex systems and modeling. The course is called Model Thinking and will start in mid to late January. Scott has a short video introduction to the course on the site.

This seems almost too good to be true. Scott is a fantastic teacher — I have been lucky to co-teach course with him at the University of Michigan and in the ICPSR summer program. He's the author of The Difference, Diversity and Complexity, and Complex Adaptive Systems: An Introduction to Computational Models of Social Life. He's a member of the American Academy of Arts and Sciences. The list goes on and on. He is a super clear thinker and has an infectious enthusiasm for modeling and complex systems.

I would recommend this course to anyone who isn't on the verge of finding a cure for cancer or solving world hunger, because otherwise whatever your doing probably won't be more impactful than taking this course.

Visualizing Your Facebook Network with Gephi

This is a visualization of my own Facebook network that I made using the (free) software Gephi and the Facebook application netvizz.  Each node in the network is one of my Facebook friends, and two friends are connected to one another if they are Facebook friends with each other.  The size of the node corresponds to the "degree" of the node, which means how many connections it has.  In this case, that means how many of my Facebook friends that person is Facebook friends with.  (Note: I deleted the names from the nodes to protect my Facebook friends' privacy).

The colors of the nodes indicate communities of friends found using a clustering algorithm based on the "modularity" of the network.  Basically what the algorithm does is try to group the nodes into communities with lots of connections within each community and not too many connection between the communities.  Even though the algorithm doesn't know anything about my friends, other than the web of connections (it doesn't even know they're people), it does a good job of picking identifying groups of my friends that belong to the same communities in real life.  For example the purple cluster in the upper right are people I know from graduate school, the little green cluster in the lower right are people from the Northwestern Institute on Complex Systems.  The big bunch in the middle are people I know from high school, with the people from the band (or band groupies) in green on the right side.  My wife is the purple node that bridges the gap between my graduate school friends and my huh school friends.

We did this as an exercise in the Social Dynamics and Networks course that I teach at Kellogg.  If you want to see how you can map your network, you can find instructions on my Kellogg website here.