Gephi forums

Data Import / Export • Exporting GEXF from Python networkx: label problem

2021-11-06T18:45:34+01:00

Dear friends,
I am building a graph with python's networkx library and then writing it out with tne nx.write_gexf(G, filename) function.

The graph is a multigraph with the nodes being authors and an edge added each time it coauthors with someone else.

Upon importing all goes well, I simply SUM the edges if there are more than one between two nodes and all the date is to be found in the data laboratory but I find that the Label column is empty and there is ANOTHER Label column added with the names.

This is how I iterate through my authors (pis) dataframe and build the nodes:

for index, row in pis.iterrows():
G.add_node(row['scid'], Label=row['name'], hindex=row['hindex'], lastyear=row['recentyear'], cits=row['cits'], role='PI', affil="IIT")

What am I doing wrong? Can't I directly have the labels filled for me?

The solution right now is manual: use the copy from another column and copy the "Label" column in the real Label column but it is a bit cumbersome.

Thanks a lot.

Statistics:Posted by rjalex — 06 Nov 2021 18:45 — Replies 0 — Views 71469

Data Import / Export • Please help importing from CVS

2021-01-04T12:57:26+01:00

Dear friends,
I have a CVS file roughly made like this:

Name, ID, Role, ManagerID
Robert, 001, Technician, 004
Ann, 002, Seller, 004
John, 003, Seller, 005
Daniela, 004, Manager, 007

From which I'd need to build a graph with nodes 001,002,003,004 and the Names as the nodes labels.
I also would like to use the Role content to partition/colour the graph.

The directed edges would show that 001 and 002 report to 004 (not quite sure if I would represent the 005 and 007 nodes since I don't have data for them but could use them to generate edges).

From the online documentation I am not sure to understand how to convert the source CSV file in such a way that it not only builds a node and an edges list, but would also bring in the nodes attributes such as Role.

Thank you very much. Happy 2021.

Statistics:Posted by rjalex — 04 Jan 2021 12:57 — Replies 0 — Views 71829

How-To and Troubleshooting • OpenGL falling back to Microsoft Generic GDI instead of Geforce

2019-11-20T12:20:57+01:00

hi folks. on load, i get an error saying

"Your OpenGL2 version (1.1.0) is too low to display the graph. Update your graphical drivers or configuration."
Current hardware:
Microsoft Corporation
GDI Genric
VersionL1.1.0;

I have a Geforce GT 710 graphics card installed on my Win10 machine with the latest NVIDIA drivers installed (v441.20). Regardless, Gephi seems to be falling back to some kind of generic graphics driver.

I have also tried forcing Gephi to use the Geforce in the NVIDIA Control Panel where under "Manage 3D settings" > "Global Settings" > "OpenGL rendering GPU" is set to "Geforce GT 710". Similarly, I have specifically add the gephi64.exe executable under the "Program Settings" tab and set it to use the Geforce GT 710.

However, I still the same error on loading Gephi. Any thoughts? Thanks!

Statistics:Posted by ervler — 20 Nov 2019 12:20 — Replies 0 — Views 109900

How-To and Troubleshooting • Gephi warnings

2019-09-20T15:55:39+01:00

I have spent a while without using Gephi. And now, when I started it:

CODE:

user@userw:~/temp/gephi/gephi-0.9.2$ ./bin/gephi user_mt-dna_GD.gephiWARNING: An illegal reflective access operation has occurredWARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/home/user/temp/gephi/gephi-0.9.2/platform/lib/boot.jar) to field java.net.URL.handlerWARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactoryWARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operationsWARNING: All illegal access operations will be denied in a future releaseInconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)' failed!user@userw:~/temp/gephi/gephi-0.9.2$

Gephi stops running. How to solve this?

Statistics:Posted by ifizer — 20 Sep 2019 15:55 — Replies 0 — Views 91251

Dynamics • Dynamic Edges from .csv import

2019-06-05T16:18:04+01:00

I have an incoming dataset for a co-inventor network. My data is in a spreadsheet (.csv) and it has a column for "InventionID", "Inventor" and "DIsclosure Date".

Each inventor has his or her own line meaning that in order to create an edgelist I need to first create an incidence matrix and then an adjacency matrix, which I'm doing in R using igraph and rgexf packages.

Here's what the incoming data looks like, you can see the multiple inventors for some inventions are given their own line for the same inventionID:

InventionId,DisclosureDate,InventorEMail,InventorCity,EndDate
81455383,3/7/2000,david.k,Beaverton, 11/1/2017
81455383,3/7/2000,ronald.s, Vancouver, 11/1/2017
81455383,3/7/2000,vladek.k,Beaverton, 11/1/2017
81455805,3/21/2000,howard.d,San Dimas, 11/1/2017
81455805,3/21/2000,paul.br,San Dimas, 11/1/2017
81456232,4/25/2000,alexey.k,San Dimas, 11/1/2017
81456285,4/27/2000,joan.v,San Dimas, 11/1/2017
81456347,5/1/2000,vladek.k,Beaverton, 11/1/2017
81456347,5/1/2000,will.al,Beaverton, 11/1/2017

I want to get to a DYNAMIC graph of co-inventor nodes wherein the edges are the inventions but I cannot figure out how to attach the DISCLOSURE DATE to the EDGE rather than to the inventor.

Here's the R script I'm using to pre-process the data. Right now it is set to attach the DisclosureDate and the EndDate to the INVENTOR (node) rather than the inventionID (Edge).

``library(igraph)
library(rgexf)
options(stringsAsFactors=FALSE) #make sure that countries shows up as characters for the nodes
dat<-read.csv(file.choose(),header=TRUE,encoding="UTF-8") #read in the raw data
incidence_matrix<-xtabs(~InventorEMail+InventionId,dat)
adjacency_matrix<-tcrossprod(incidence_matrix)
g<-graph.adjacency(adjacency_matrix,mode="undirected") #creates graph object for undirected graph
#Time to Link "City" to "Inventor"
ix<-match(V(g)$name,dat$InventorEMail)
V(g)$city<-dat$InventorCity[ix]
set.vertex.attribute(graph=g,name='city',value=dat$InventorCity[ix])
#TimeStamps
V(g)$start_date2<-dat$DisclosureDate[ix]
set.vertex.attribute(graph=g,name='start_date2',value=dat$DisclosureDate[ix])
V(g)$end_date2<-dat$EndDate[ix]
set.vertex.attribute(graph=g,name='end_date2',value=dat$EndDate[ix])
#Process for Gephi
g2<-simplify(g,remove.loops=TRUE,remove.multiple = FALSE) #Remove Loops from Dataset, keep duplicates
network.gexf<-igraph.to.gexf(g2)
f<-file("network.gexf")
writeLines(network.gexf$graph,con=f)``

Statistics:Posted by godot90 — 05 Jun 2019 16:18 — Replies 0 — Views 107322

Visual Results • Export to Graphic with stable(!) positions

2019-05-31T14:35:50+01:00

Hi,

I use gephi to create a dynamic Network. Now I want to create "snapshots" of this network at different points in time. I use the Gephi-Toolkit for that as I want to create reproducible results. Most importantly, I'd like to keep the once computed and exported positions of the nodes stable.

This work quite well - but it has one glitch: In my networks some nodes appear later and they have an outer position. The problem is, that Gephi seems to recalculate the positions in the canvas relatively to the most out-lying nodes, even though the positions are stored in its (x,y)-coordinates.

As a result the positions of my nodes are not always stable.

Are there any hints or proposals how I could fix the translation of Gephi's coordinates to the Export? I tried to use the "AppearanceContronler" and the Preview-API for that. But I did not any clues how I could manage that.

Any help is appreciated!

Tino

Statistics:Posted by tschoellhorn — 31 May 2019 14:35 — Replies 0 — Views 106501

Layouts • Radial labels for Circular Layout

2019-03-06T10:40:07+01:00

Is there any way to orient the node labels of a circular layout radially and not all at the same (horizontal) orientation?

Thank you

Statistics:Posted by rjalex — 06 Mar 2019 10:40 — Replies 0 — Views 115078

Visual Results • Please help with palettes

2019-03-02T18:20:57+01:00

I have a 8000nodes/90000 edges multigraph.
The edges have a "year" parameter.
I would like to have 2019 edges in red and less and less red until 2010 then before that everything in grey.
I am not finding a way to generate a decreasing shade of colour for a given number of steps and use it as a palette.
Any ideas?
Thank you

Statistics:Posted by rjalex — 02 Mar 2019 18:20 — Replies 0 — Views 74270

Filtering, Ranking & Interacting with the graph • Exploring a multigraph in time

2019-03-02T12:07:57+01:00

Dear friends,
I have built a multigraph with networkx and exported it to GEXF.

The nodes are authors of scientific papers and each edge connects to a coauthor for a given publication.

So for example I could have A and B coauthoring three papers in 2019, 2018 and 2017 and this would appear as two nodes and three edges between them.

The graph is medium sized, approx 10.000 authors and 90.000 edges.

What would you suggest to explore the graph time wise? Is there a way to have a slider from 1990 to 2019 and while sliding it only show edges for that year?

I can do this with filters but need a way for end users that do not know how to use Gephi to do the same.

Also another question.

What would be the easiest way of "summing" all edges into one with the weight being the added number of edges?

Thank you very much.

Statistics:Posted by rjalex — 02 Mar 2019 12:07 — Replies 0 — Views 110594

How-To and Troubleshooting • Optimizing on esacore Mac with 16GB

2019-02-24T20:58:48+01:00

Dear friends,
I have a new MacBook with an i7 esacore 2.6GHz and 16GB RAM (and Radeon Pro 560X).

I am working with medium sized graphs (30-50k nodes - 200-500k edges).

java -version
java version "1.8.0_202-ea"
Java(TM) SE Runtime Environment (build 1.8.0_202-ea-b03)
Java HotSpot(TM) 64-Bit Server VM (build 25.202-b03, mixed mode)

Gephi 0.9.2 works but kind of hangs with the largest tasks.

Question a) Do I need to install an older Java (1.7.x) version?

Question b) If I install a 1.7 JDK should I go for a 64bit version? Upon reading the install notes it seems that if you install a back level JDK the older JRE coming with it does NOT get installed. Does Gephi need a JDK or a JRE?

Question c) Provided a get the right 64 bit java installed correctly, how do I make sure Gephi and only Gephi points to it? Not sure I understand what incantation to place info Gephi.conf

Question d) For this 16GB machine which I'll use heavily for Gephi what are the recommended values for max and min RAM for both a 32 and a 64bit java?

Thank you very much in advance.

Statistics:Posted by rjalex — 24 Feb 2019 20:58 — Replies 0 — Views 94352

Data Import / Export • Adjacency list, but all combinations

2019-01-31T13:19:10+01:00

I have tried looking for an answer, but to no avail. My problem is the following: I have a number of names and I would like to construct a network of with their connections. Generally, they work in groups of three. So, let's assume they follow this scheme:

CODE:

ROW 1: Alice, Bob, CarolROW 2: John, Kate, Laura

My problem is that, the way I understand it, this would make Alice-> Bob; Alice -> Carol. Not, however Bob -> Carol.

In order to do that right from the outset, I would need to have additional rows with the different combinations. In other words, I would need:

CODE:

ROW 1: Alice, Bob, CarolROW 2: Bob, Alice, CarolROW 3: Carol, Alice, Bob

I am not sure, however, how this could be done. Can anybody suggest a solution?

Thanks!

Statistics:Posted by CaseLawMiner — 31 Jan 2019 13:19 — Replies 0 — Views 80457

Data Import / Export • How do I translate this list into a network in gephi?

2019-01-29T02:15:13+01:00

Hello,

I need your help with the following.

I have a list of more than 10,000 business projects. Each project has several participants and I want to analyze the collaboration networks of these participants.

The data is organized in a .csv file in the following way:

Project 1: Company 1; Company 2; Company 3 *
Project 2: Company 3; Company 5; Company 6; Company 10
Project 3: Company 10; Company 1

* It means that in project 1 the links are (Company 1-Company 2, Company 1- Company 3, Company 2-Company 3). etc.

How do I translate this list into a network in gephi?
Is there any way to enter the data in this format list? Or should I build an adjacency list or a quadratic matrix? Is there a quick and automatic way to move from this list to an adjacency list?
Any guidance will be welcome!

Thank you !

Statistics:Posted by cecitomassini — 29 Jan 2019 02:15 — Replies 0 — Views 72945

Plugins, presets and filters • Geo layout

2018-09-17T06:02:11+01:00

Friends I tried many a times for visualization of geographical map using Geo-Layout, but could not succeed. The nodes and edges files are attached here. Please help in developing geo map.

Regards
Singh

nodes - Copy.csv

edges - Copy.csv

Statistics:Posted by nirmal02 — 17 Sep 2018 06:02 — Replies 4 — Views 104587

How-To and Troubleshooting • Preview Settings Management

2018-09-12T22:12:04+01:00

Hi

I asked the question back in Jan - but no reply. Try again

New to Gephi (0.9.2 running on Win10).

In Preview Settings I click the button top right/Save preset.

But how do I create a new preset? I've occasionally seen, and used, a new preset naming dialogue but I can't
consistently repeat its appearance. I've tried double clicking and RH clicking the Save Preset button to no avail.

Also how do I delete a preset no longer required?

Regards WeeJimmy

Statistics:Posted by WeeJimmy — 12 Sep 2018 22:12 — Replies 2 — Views 51396

How-To and Troubleshooting • File Saving

2018-06-21T11:58:50+01:00

Is there a way to save that retains my Partition settings, both in Node colors and Filters?

Statistics:Posted by beachcm65 — 21 Jun 2018 11:58 — Replies 0 — Views 90974