rgexf: Build, Import and Export GEXF Graph Files

The first R package to work with GEXF graph files (used in Gephi and others). rgexf allows the user to quickly build/read graph files, including:

Nodes/edges attributes,
GEXF viz attributes (such as color, size, and position),
Network dynamics (for both edges and nodes, including spells), and
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 0.16.2 (2021-08-10)

New features and changes

We now have a hex sticker!
Users can now cite properly rgexf with JOSS (see citation(package="rgexf")).
Added a few extra breaks across the examples (suggested by @corneliusfritz).
Improved documentation regarding spells and dynamic graphs (suggested by @jonjoncardoso).
New head() function allows a glimpse of the n first nodes/edges.

Bug fixes

Passing colors with four values (alpha) no longer fails during checks. (reported by @IsabelFE).
The summary function prints nodes’ attributes as expected.
Hex colors now work (#41 reported by @milnus).
gexf.to.igraph correctly processes edge attributes (#38 reported by @balachia).
Time range is now correctly computed (#19).
Non-integer ids were incorrectly processed when reading GEXF files.

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

And the actual R package:

Vega Yon G, Fábrega Lacoa J, Kunst J (2021). _netdiffuseR: Build,
Import and Export GEXF Graph Files_. doi: 10.5281/zenodo.5182708 (URL:
https://doi.org/10.5281/zenodo.5182708), R package version 0.16.2,
<URL: 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)'.

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)

An live version of the figure is available here.

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="2021-08-12">
##     <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="100" y="76.2515713120152" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="2" label="pedro">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="-100" y="-100" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="3" label="matthew">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="-33.934012157033" y="55.4559262362359" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="4" label="carlos">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="4.50330959513599" y="100" z="0"/>
##         <viz:size value="10"/>
##       </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="2021-08-12">
##     <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="93.5382155239999" y="100" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="2" label="pedro" start="13" end="13">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="-100" y="-45.2089025903595" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="3" label="matthew" start="2" end="13">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="100" y="-25.9442855933132" z="0"/>
##         <viz:size value="10"/>
##       </node>
##       <node id="4" label="carlos" start="2" end="13">
##         <viz:color r="255" g="99" b="71" a="1"/>
##         <viz:position x="-10.7885944593362" y="-100" z="0"/>
##         <viz:size value="10"/>
##       </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="2021-08-12">
##     <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="-52.8911775840454" y="-100" z="0"/>
##         <viz:size value="10"/>
##       </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="-79.9134848326296" y="-8.92670659506044" z="0"/>
##         <viz:size value="10"/>
##       </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="100" y="100" z="0"/>
##         <viz:size value="10"/>
##       </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="-100" y="-40.0433660159618" z="0"/>
##         <viz:size value="10"/>
##       </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

Session info

devtools::session_info()

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 4.1.0 (2021-05-18)
##  os       Ubuntu 18.04.5 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language en_US:en                    
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/Los_Angeles         
##  date     2021-08-12                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package     * version  date       lib source        
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##  glue          1.4.2    2020-08-27 [1] CRAN (R 4.1.0)
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##  htmltools     0.5.1.1  2021-01-22 [1] CRAN (R 4.1.0)
##  httpuv        1.6.1    2021-05-07 [1] CRAN (R 4.1.0)
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##  magrittr      2.0.1    2020-11-17 [1] CRAN (R 4.1.0)
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##  remotes       2.3.0    2021-04-01 [1] CRAN (R 4.1.0)
##  rgexf       * 0.16.2   2021-08-12 [1] local         
##  rlang         0.4.11   2021-04-30 [1] CRAN (R 4.1.0)
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## [3] /usr/lib/R/site-library
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