GEPHI - Network visualization tutorial [HD]

[@MartinGrandjean]

New video with voiceover here: kzbin.info/www/bejne/fYnXk39ultujn80 ! 😃

[@khadijahmakhadmi238]

Honestly... god bless you. You have zero idea how much you helped me.

[@lucasadje]

I was wondering what software you used to overlay the map and the network.

[@MartinGrandjean]

Hi, it's Inkscape, an open-source drawing software: inkscape.org/

[@johirislam8174]

One problem I also feel very much,which kind of formated file I can open into gephi?? I want to visualize my gene network that i generated from network analyst web platform.And the file format is .sif.

[@RobertAlexanderRM]

Very interesting but an audio with you explaining why you are doing certain things would have added a lot. Thank you.

[@MartinGrandjean]

Thank you for your interest. I'm thinking about producing a new video/set of videos with a descriptive audio. This summer maybe?

[@RobertAlexanderRM]

Will send you cool beer to help you :) @@MartinGrandjean

[@22tabahgayuhaditama40]

From Senen, Jakarta, Mantap!!

[@CuriousMelya]

dari klaten ui

[@saketbhojane5697]

Amazing. One video, encompassing everything. Keep making such tutorials for other tools too please :D

[@MartinGrandjean]

Many thanks!

[@jrb2882]

VEry good tutorial thanks so much for it. How do you adjust sizw the graph to the map size or where can i fin suitable maps for gephi??

[@guzellkerem]

Noverlap plugin is not valid anymore for 0.9.2 how can ı fix it ?

[@MartinGrandjean]

It's a built-in feature in the new version, normally. You don't find it in the "Layout" panel bottom-left?

[@moderato9264]

Amazing tutorial! I am new to gephi and started using gephi 0.9.0 recently. Some plugins like graph streaming is not found in gephi 0.9.0. The website only provide its version supporting 0.8.2 beta. Where can I find this plugin? Or it's already integrated into 0.9.0? Thanks!

[@MartinGrandjean]

+林中一 Thank your for your interest! You're right, this tutorial has been published using 0.8.2. As the plugins for the new 0.9.0 version are still under development, I recommend installing Gephi 0.8.2 instead (on Gephi Download page, click on "Download older versions").

[@moderato9264]

+Martin Grandjean OK thanks! BTW are you still maintaining the plugin store for 0.8.2? I try to update the plugins but got an 403 error on Gephi.

[@MartinGrandjean]

林中一 There's indeed a connexion problem these days (/weeks/months), because of the transition...

[@mollywillo]

My exported SVG did not include any aspects of the visualization (edge colors, node size, etc.) when viewed in Inkscape. But I haven't ever worked with Inkscape before, so that might be part of the issue.

[@MartinGrandjean]

Hi. Never had this issue before, so hard to tell where the problem is. Note that you can open an SVG file with your web browser, try that to see if your file contains something.

[@pushpadm4755]

sir is it helpful for pubmed data?

[@ouigourtube]

Bonjour Martin, j'ai essayé de tout faire pareil. Mais déjà lorsque j'ai essayé d'importer Noverlap, il n'apparaît pas dans ma liste (qui contient que 17 plugin). Et puis, surtout lorsque j'importe mon fichier csv (les liens de sites internet et les informations concernant chaque site), dans les attributs, on m'affiche pour chaque label (liens, type, propriétaires, langues...Etc) presque pas de valeur, mais un vide s'affiche avec plus de 90% comme label. Je ne comprends pas où est l'erreur. Vous-voyez l'erreur depuis mon explication?

[@MartinGrandjean]

Bonjour, merci pour le message ! J'ai actuellement des soucis avec Noverlap sur Gephi 0.9.1 (est-ce que vous êtes bien sur cette nouvelle version ou sur la 0.8.2, sur laquelle il devrait y avoir moins de problèmes ?). Dans tous les cas, c'est bien dans la fenêtre "available plugins" qu'il faut chercher, après avoir vérifié qu'il n'est pas déjà installé. Pour l'importation de vos données, il peut s'agir d'un problème de compatibilité de l'encodage (par exemple des caractères spéciaux), mais c'est plus souvent dû à un mauvais réglage des paramètres d'imports. Mais je ne vois pas ni d'erreur ni de solution miracle, si ce n'est un classique du genre : désinstaller l'application et la réinstaller comme neuve...

[@ouigourtube]

Merci de votre retour. Oui, j'utilise la toute nouvelle version. Comme vous dites, j'ai essayé de désinstaller et réinstaller au moins dix fois J'ai passé trois jours à le comprendre en essayant tout. J'ai même essayé de faire deux fichiers séparés (l'un est liens comprenant que trois colons dont source (le numéro de chaque target), target (les liens des sites web) et weight; le second contient les attributs correspondant à chaque target (pays, langues...). Mais le résultat est le même, un attribut qui s'appelle "vide" prend toujours 90% de valeur, les autres (si c'est pays par exemple, USA 6%, France 3%...). Malgré toutes les lectures que j'ai trouvé sur internet sur le fonctionnement, je n'ai pas réussi à résoudre le problème. D'autant plus, je trouve qu'il n'y a pas de manuel sur la préparation du fichier csv et son importation, pourtant c'est une étape clé du Gephi.

[@rewatthapa2327]

Hey Martin!! Thank you for a great tutorial on Gephi. I have a question though after you have generated the unipartite graph from the bipartite graph, for calculating the degree centrality of new graph you use the statistics option 'weighted graph' instead of degree. could you please explain me the reason behind it? Thank you

[@MartinGrandjean]

Hi! When it comes to the 1-mode graph, some nodes may have been connected to the same removed nodes more than once. That's why you have to use a weighted degree calculation to take into accounts the fact that some edges don't have a weight of 1 anymore but of 2 or 3.

[@rewatthapa2327]

Thank you Martin for the clarification

[@PeniHausia]

Hi - I'm new to gephi and just recently learning how to use it (0.9.1). I was wondering how did you get your country coordinates (latitude & longitude) so I can used it with my own data. And then how did you zoom it? I'm using Win OS 10.

[@MartinGrandjean]

The city coordinates have been retrieved manually (Google Map is helpful for that). I don't understand what you're meaning by "zoom it".

[@PeniHausia]

I saw your video sometimes you zoom the nodes and edges to see the names more clearly (4:41 & 7:07). I followed exactly the way you do it. When I tried to zoom, my laptop (mouse) can't do it. I was wondering how did you do it. Thank you so much for the coordinates, I'm working on it with my own data.

[@TechSupport100]

He probably zoomed in the screen recorder he was using (like Camtasia), not in Gephi.

[@MartinGrandjean]

Well, no, I zoomed in Gephi, 2 fingers on the trackpad when the cursor is on the graph area. But every PC is different... see with you own configurations.

[@raphaelbonillo2192]

Hi, could you help me? Is possible to set up a benchmark between 3 brands in the same visualization?

[@MartinGrandjean]

Hi, could you please develop your question? I'm not sure to understand your need.

[@raphaelbonillo2192]

Of course yes. I've already got facebook''s data about an specific Brand, using Netvizz. It's a Software company. So I realized that some users in this company page are Surfing between another companies, on the facebook too, problably they are looking for similar services offered by their. Is possible to load 3 different GDF files in one Gephi instance? Matching the same users around this pages?

[@MartinGrandjean]

Of course, if the users are identified with the same usernames/ID, Gephi will recognize them as a single node.

[@anjaleesyangbo1479]

Whenever I try to download the Noverlap plugin it doesn't appear in the available plugins? Is there something that I can do to fix it?

[@MartinGrandjean]

Oh, looks like you're not the only one to have that issue. As I had a few problems with this plugin weeks ago, I assume (and hope) the plugin is under development/update.

[@Menino01]

No sound, why?

[@MartinGrandjean]

That's a way to make this tutorial available for non-english speakers (and for people working without headphones), with all the informations displayed during the tutorial (the video was produced to complement this tutorial: www.martingrandjean.ch/gephi-i...)

[@productnerd]

Thank you for the fantastic video Martin! It has been so helpful to get me started. Just a quickie question; Is there a reason you are first using the Fruchterman Reingold and then the Force Atlas in the first example? Thanks!

[@MartinGrandjean]

+Maria Papadopoulou I'm very happy if it helped! As the Force Atlas is a very "strong" algorithm, it sometimes tangle some groups of nodes in the first steps of the spatialization. I prefer to use a "softer" algorithm like Fruchterman Reingold to untangle everything and to let the communities find their places before forcing the graph to become more readable, more stretched.

[@productnerd]

+Martin Grandjean yep that makes total sense. Ill adopt that practice from you then. ;) Thanks again!

[@fangxu2]

Great video! Can you share the Excel file you used in the video? Also, how did you find raw data files like this?

[@MartinGrandjean]

+Fang Xu Thanks. You'll find the 4 Excel files under point 2.3 here: www.martingrandjean.ch/gephi-introduction/ They've been 'constructed' for the tutorial.

[@fangxu2]

+Martin Grandjean Awesome！Your blog is really informative. I just started to learn Gephi. Can I also use Gephi to compare multiple network diagrams generated from different data? I really need some digital method to do such cross-case analyses.

[@MartinGrandjean]

+Fang Xu Of course, but if you want to compare them precisely, your different dataset will have to be based on the same kind of data (like different theatre pieces - www.martingrandjean.ch/network-visualization-shakespeare/ - or tweets on different hashtags, letters exchanges during a certain period, etc.).

[@fangxu2]

+Martin Grandjean That post is helpful! Yet I am wondering if Gephi can categorize these diagrams by customized criteria such as similarities in nodes, links, and link weights. I've been trying hard to find a visualized algorithm to analyze graph similarity.

[@MartinGrandjean]

Fang Xu Gephi won't do that job, but you can easily download the CSV nodes/edges files from Gephi after having calculated the weights, degrees etc. and make the comparisons and other statistical analysis in Excel.

[@himadrisdebnath]

I am following your tutorial with 0.9.1 version , and I am not able to find the partition or the ranking button.

[@MartinGrandjean]

Hi, you're right, the partition and ranking buttons have been merged into a new one in v.0.9.1: "Attribute" (in fact, this is the most "visible" interface difference between 0.8.2 and this new version).

[@himadrisdebnath]

Oh Yes. I re installed it again . It is now being showed.

[@sidydiakhate609]

Hello, Martin thank for all the responses what version do you think is the most complete to use for Data viz o.9.1 or o.8.2?? Many thanks

[@MartinGrandjean]

Well, I've completely switched to 0.9.1 now, most of the plugins that are useful to me are compatible with this new version and the compatibility with recent OS is much better.

[@sidydiakhate609]

Martin Grandjean thank you

[@monakhneisser2941]

Hey! there is no sound

[@MartinGrandjean]

Yep, as I said in other comments here, that's a way to make this tutorial available for non-english speakers (and for people working without headphones), with all the informations displayed during the tutorial (and a comprehensive tutorial online to complete the video: www.martingrandjean.ch/gephi-introduction)

[@EmmanuelNwofe]

The audio is lost!

[@MartinGrandjean]

Hey, thank you for your interest in this tutorial. There's no audio, that's a way to make this tutorial available for non-english speakers (and for people working without headphones), with all the informations displayed during the tutorial (and a comprehensive tutorial online to complete the video: www.martingrandjean.ch/gephi-introduction). Thanks for your understanding, and feel free to follow the tutorial listening to your own favorite music ;)

[@MichaelMenke]

No sound!

[@MartinGrandjean]

Yep, as I said in other comments here, that's a way to make this tutorial available for non-english speakers (and for people working without headphones), with all the informations displayed during the tutorial (and a comprehensive tutorial online to complete the video: www.martingrandjean.ch/gephi-introduction)

[@nielsandreasamstrup6128]

Roman sent me here

[@TheCyberklutz]

I assume your audience has to guess what's going on! Don't waste peoples time.

[@MartinGrandjean]

Hi, this video is mostly used as a complement to this full tutorial: www.martingrandjean.ch/gephi-introduction, not as the main explanation itself. I chose not to add an audio track and subtitles because it's an helping tool and not a tutorial backbone. Sorry for misunderstanding, and feel free to ask me anything unclear about Gephi.

[@brigidm6279]

@@MartinGrandjean You are very patient with rude people!

[@MartinGrandjean]

@@brigidm6279 😉

[@istuyapi6447]

useless without audio

[@MartinGrandjean]

... thank you for your consideration for my work... There's no sound because this video has been made to accompany a complete tutorial (www.martingrandjean.ch/gephi-introduction/).