rgexf: Build, Import and Export GEXF Graph Files

[!NOTE] How to cite rgexf. If you use rgexf in published work, please cite it:

Vega Yon GG (2021). Building, Importing, and Exporting GEXF Graph Files with rgexf. Journal of Open Source Software, 6(64), 3456. doi:10.21105/joss.03456

Run citation("rgexf") in R for the BibTeX entry.

The first R package to work with GEXF graph files (used in Gephi and others). rgexf allows reading and writing graph files, including:

1. Nodes/edges attributes,

2. GEXF viz attributes (such as color, size, and position),

3. Network dynamics (for both edges and nodes, including spells) and

4. Edges weighting.

Users can build/handle graphs element-by-element or through data-frames, visualize the graph on a web browser through sigmajs javascript gexf-js library and interact with the igraph package.

Changes in rgexf version 0.16.4

New features and changes

• plot.gexf() now renders graphs as an interactive htmlwidget powered by sigma.js v3 and graphology. Node positions, colours, and sizes are read from the viz:* attributes in the GEXF document.

• New sigmajs() function creates a sigma.js htmlwidget from a gexf object or a path to a .gexf file. Shiny helpers sigmajsOutput() and renderSigmajs() are also available.

• The legacy gexf-js file-server renderer is preserved as plot_gexfjs(). The gexfjs() htmlwidget (inline iframe approach) is likewise kept for backward compatibility.

• gexfjs() now accepts a gexf object in addition to a file path, matching sigmajs().

• gexfjs() has an explicit sizing policy: the widget now defaults to the full available width and a height of 600px (50% taller than before) in knitr documents, the browser, and Shiny alike. Both gexfjs() and sigmajs() honor user-supplied width/height, and their documented defaults were clarified.

Bug fixes

• The gexfjs() widget rendered an empty main canvas: the bundled config.js (which sets zoomLevel, showEdges, and other gexf-js defaults) was never loaded into the iframe, making every screen coordinate NaN.

• Icons and images in the gexfjs() widget (zoom, lens, edge buttons, search icon, Gephi logo) did not display: relative url(...) references in the CSS cannot resolve inside a srcdoc iframe, so images are now inlined as base64 data URIs.

• The gexfjs() widget’s node-attribute panel was blank and search did not work: the generated DOM was missing the #leftcontent element, the search form id had a typo (reacherche), and the autocomplete list was clipped by the title bar.

More in the NEWS.md file.

Installation

To install the latest version of rgexf, you can use devtools

library(devtools)
install_github("gvegayon/rgexf")

The more stable (but old) version of rgexf can be found on CRAN too:

install.packages("rgexf")

Citation

citation(package="rgexf")

To cite rgexf in publications use the following paper:

  Vega Yon G (2021). "Building, Importing, and Exporting GEXF Graph
  Files with rgexf." _Journal of Open Source Software_, *6*, 3456.
  doi:10.21105/joss.03456 <https://doi.org/10.21105/joss.03456>,
  <https://doi.org/10.21105/joss.03456>.

And the actual R package:

  Vega Yon G, Fábrega Lacoa J, Kunst J (????). _netdiffuseR: Build,
  Import and Export GEXF Graph Files_. doi:10.5281/zenodo.5182708
  <https://doi.org/10.5281/zenodo.5182708>, R package version 0.16.4,
  <https://github.com/gvegayon/rgexf>.

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.

Who uses rgexf?

usescout tracks where rgexf is used: GitHub repositories, CRAN packages and papers, including papers that use it without citing it. The current list, with the exact place each one was found, is in the usage report; the data lives in the usescout branch. If you use rgexf in published work, please cite it.

Examples

Example 1: Importing GEXF files

We can use the read.gexf function to read GEXF files into R:

# Loading the package
library(rgexf)

g <- system.file("gexf-graphs/lesmiserables.gexf", package="rgexf")
g <- read.gexf(g)
head(g) # Taking a look at the first handful

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.3" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd">
  <meta lastmodifieddate="2016-11-09">
    <creator>Gephi 0.9</creator>
    <description/>
  </meta>
  <graph defaultedgetype="undirected" mode="static">
    <attributes class="node" mode="static">
      <attribute id="modularity_class" title="Modularity Class" type="integer"/>
    </attributes>
    <nodes>
      <node id="11" label="Valjean">
        <attvalues>
          <attvalue for="modularity_class" value="1"/>
        </attvalues>
        <viz:size value="100.0"/>
        <viz:position x="-87.93029" y="6.8120565"/>
        <viz:color r="245" g="91" b="91"/>
      </node>
      <node id="48" label="Gavroche">
        <attvalues>
          <attvalue for="modularity_class" value="8"/>
        </attvalues>
        <viz:size value="61.600006"/>
        <viz:position x="387.89572" y="-110.462326"/>
        <viz:color r="91" g="245" b="91"/>
      </node>
      <node id="55" label="Marius">
        <attvalues>
          <attvalue for="modularity_class" value="6"/>
        </attvalues>
        <viz:size value="53.37143"/>
        <viz:position x="206.44687" y="13.805411"/>
        <viz:color r="194" g="91" b="245"/>
      </node>
      <node id="27" label="Javert">
        <attvalues>
          <attvalue for="modularity_class" value="7"/>
        </attvalues>
        <viz:size value="47.88571"/>
        <viz:position x="-81.46074" y="204.20204"/>
        <viz:color r="91" g="245" b="194"/>
      </node>
      <node id="25" label="Thenardier">
        <attvalues>
          <attvalue for="modularity_class" value="7"/>
        </attvalues>
        <viz:size value="45.142853"/>
        <viz:position x="82.80825" y="203.1144"/>
        <viz:color r="91" g="245" b="194"/>
      </node>
      <node id="23" label="Fantine">
        <attvalues>
          <attvalue for="modularity_class" value="2"/>
        </attvalues>
        <viz:size value="42.4"/>
        <viz:position x="-313.42786" y="289.44803"/>
        <viz:color r="91" g="194" b="245"/>
      </node>
            ...
     </nodes>
    <edges>
      <edge id="0" source="1" target="0"/>
      <edge id="1" source="2" target="0" weight="8.0"/>
      <edge id="2" source="3" target="0" weight="10.0"/>
      <edge id="3" source="3" target="2" weight="6.0"/>
      <edge id="4" source="4" target="0"/>
      <edge id="5" source="5" target="0"/>
            ...
     </edges>
  </graph>
</gexf>

Moreover, we can use the gexf.to.igraph() function to convert the gexf object into an igraph object:

library(igraph)

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

ig <- gexf.to.igraph(g)

op <- par(mai = rep(0, 4)) # Making room
plot(ig)

par(op)

Using the plot.gexf method–which uses the gexf-js JavaScript library–results in a Web visualization of the graph, like this:

plot(g)

Example 2: Static net

# Creating a group of individuals and their relations
people <- data.frame(matrix(c(1:4, 'juan', 'pedro', 'matthew', 'carlos'),ncol=2))
people

  X1      X2
1  1    juan
2  2   pedro
3  3 matthew
4  4  carlos

# Defining the relations structure
relations <- data.frame(matrix(c(1,4,1,2,1,3,2,3,3,4,4,2), ncol=2, byrow=T))
relations

  X1 X2
1  1  4
2  1  2
3  1  3
4  2  3
5  3  4
6  4  2

# Getting things done
write.gexf(people, relations)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2026-07-08">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="static" defaultedgetype="undirected">
    <nodes>
      <node id="1" label="juan">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="163.952692888871" y="100.415277363797" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="235.61426657648" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="189.744021945668" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" weight="1"/>
      <edge id="1" source="1" target="2" weight="1"/>
      <edge id="2" source="1" target="3" weight="1"/>
      <edge id="3" source="2" target="3" weight="1"/>
      <edge id="4" source="3" target="4" weight="1"/>
      <edge id="5" source="4" target="2" weight="1"/>
    </edges>
  </graph>
</gexf>

Example 3: Dynamic net

# Defining the dynamic structure, note that there are some nodes that have NA at the end.
time<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time

     [,1] [,2]
[1,]   10   12
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA

# Getting things done
write.gexf(people, relations, nodeDynamic=time)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2026-07-08">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="dynamic" start="2" end="13" timeformat="double" defaultedgetype="undirected">
    <nodes>
      <node id="1" label="juan" start="10" end="12">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro" start="13" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-116.286814488559" y="-48.8491528929603" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew" start="2" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="193.001175103911" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos" start="2" end="13">
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="-174.022122416047" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" weight="1"/>
      <edge id="1" source="1" target="2" weight="1"/>
      <edge id="2" source="1" target="3" weight="1"/>
      <edge id="3" source="2" target="3" weight="1"/>
      <edge id="4" source="3" target="4" weight="1"/>
      <edge id="5" source="4" target="2" weight="1"/>
    </edges>
  </graph>
</gexf>

Example 4: More complex… Dynamic graph with attributes both for nodes and edges

First, we define dynamics

time.nodes<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time.nodes

     [,1] [,2]
[1,]   10   12
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA

time.edges<-matrix(c(10.0,13.0,2.0,2.0,12.0,1,5,rep(NA,5)), nrow=6, ncol=2)
time.edges

     [,1] [,2]
[1,]   10    5
[2,]   13   NA
[3,]    2   NA
[4,]    2   NA
[5,]   12   NA
[6,]    1   NA

Now we define the attribute values

# Defining a data frame of attributes for nodes and edges
node.att <- data.frame(letrafavorita=letters[1:4], numbers=1:4, stringsAsFactors=F)
node.att

  letrafavorita numbers
1             a       1
2             b       2
3             c       3
4             d       4

edge.att <- data.frame(letrafavorita=letters[1:6], numbers=1:6, stringsAsFactors=F)
edge.att

  letrafavorita numbers
1             a       1
2             b       2
3             c       3
4             d       4
5             e       5
6             f       6

# Getting the things done
write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges,
           edgesAtt=edge.att, nodeDynamic=time.nodes, nodesAtt=node.att)

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.3" xmlns:viz="http://www.gexf.net/1.3/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.3 http://www.gexf.net/1.3/gexf.xsd" version="1.3">
  <meta lastmodifieddate="2026-07-08">
    <creator>NodosChile</creator>
    <description>A GEXF file written in R with "rgexf"</description>
    <keywords>GEXF, NodosChile, R, rgexf, Gephi</keywords>
  </meta>
  <graph mode="dynamic" start="1" end="13" timeformat="double" defaultedgetype="undirected">
    <attributes class="node" mode="static">
      <attribute id="att1" title="letrafavorita" type="string"/>
      <attribute id="att2" title="numbers" type="integer"/>
    </attributes>
    <attributes class="edge" mode="static">
      <attribute id="att1" title="letrafavorita" type="string"/>
      <attribute id="att2" title="numbers" type="integer"/>
    </attributes>
    <nodes>
      <node id="1" label="juan" start="10" end="12">
        <attvalues>
          <attvalue for="att1" value="a"/>
          <attvalue for="att2" value="1"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="250" y="241.156927125917" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="2" label="pedro" start="13" end="13">
        <attvalues>
          <attvalue for="att1" value="b"/>
          <attvalue for="att2" value="2"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="102.288482685844" y="-250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="3" label="matthew" start="2" end="13">
        <attvalues>
          <attvalue for="att1" value="c"/>
          <attvalue for="att2" value="3"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="-250" y="250" z="0"/>
        <viz:size value="125"/>
      </node>
      <node id="4" label="carlos" start="2" end="13">
        <attvalues>
          <attvalue for="att1" value="d"/>
          <attvalue for="att2" value="4"/>
        </attvalues>
        <viz:color r="255" g="99" b="71" a="1"/>
        <viz:position x="42.176120373259" y="-45.0467720735" z="0"/>
        <viz:size value="125"/>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="1" target="4" start="10" end="5" weight="1">
        <attvalues>
          <attvalue for="att1" value="a"/>
          <attvalue for="att2" value="1"/>
        </attvalues>
      </edge>
      <edge id="1" source="1" target="2" start="13" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="b"/>
          <attvalue for="att2" value="2"/>
        </attvalues>
      </edge>
      <edge id="2" source="1" target="3" start="2" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="c"/>
          <attvalue for="att2" value="3"/>
        </attvalues>
      </edge>
      <edge id="3" source="2" target="3" start="2" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="d"/>
          <attvalue for="att2" value="4"/>
        </attvalues>
      </edge>
      <edge id="4" source="3" target="4" start="12" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="e"/>
          <attvalue for="att2" value="5"/>
        </attvalues>
      </edge>
      <edge id="5" source="4" target="2" start="1" end="13" weight="1">
        <attvalues>
          <attvalue for="att1" value="f"/>
          <attvalue for="att2" value="6"/>
        </attvalues>
      </edge>
    </edges>
  </graph>
</gexf>

Code of Conduct

We welcome contributions to rgexf. Whether reporting a bug, starting a discussion by asking a question, or proposing/requesting a new feature, please go by creating a new issue here so that we can talk about it.

Please note that the rgexf project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms