The first R package to work with GEXF graph files (used in Gephi and others). rgexf
allows reading and writing 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.
More in the NEWS.md file.
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(package="rgexf")
in publications use the following paper:
To cite rgexf
Vega Yon, G. G., (2021). Building, Importing, and Exporting GEXF
6(64), 3456,
Graph Files with rgexf. Journal of Open Source Software, ://doi.org/10.21105/joss.03456
https
:
And the actual R package
Vega Yon G, Fábrega Lacoa J, Kunst J (2024). _netdiffuseR: Build,
:10.5281/zenodo.5182708
Import and Export GEXF Graph Files_. doi<https://doi.org/10.5281/zenodo.5182708>, R package version 0.17.0,
<https://github.com/gvegayon/rgexf>.
in BibTeX format, use 'print(<citation>,
To see these entries bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.
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:
: 'igraph'
Attaching package
'package:stats':
The following objects are masked from
decompose, spectrum
'package:base':
The following object is masked from
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)
A live version of the figure is available here.
# Creating a group of individuals and their relations
people <- data.frame(matrix(c(1:4, 'juan', 'pedro', 'matthew', 'carlos'),ncol=2))
people
X1 X21 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 X21 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="2024-06-30">
<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="79.2065507374859" y="-250" 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="91.9438021126364" 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="-79.815764224491" 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="194.911331255884" 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>
# 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="2024-06-30">
<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="-250" y="-250" 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="23.8452238193327" y="113.652288092202" 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="77.7158886485609" y="-219.373757312507" 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>
First, we define dynamics
1] [,2]
[,1,] 10 12
[2,] 13 NA
[3,] 2 NA
[4,] 2 NA [
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 numbers1 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 numbers1 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="2024-06-30">
<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="116.263539042396" 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="-162.569255531004" 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="142.556872059596" y="89.0845907381178" 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>
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
devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value4.4.0 (2024-04-24)
version R version 22.04.4 LTS
os Ubuntu 64, linux-gnu
system x86_
ui X11language (EN)
-8
collate en_US.UTF-8
ctype en_US.UTF/Denver
tz America2024-06-30
date 3.1.1 @ /usr/bin/ (via rmarkdown)
pandoc
─ Packages ───────────────────────────────────────────────────────────────────* version date (UTC) lib source
package 1.1.0 2024-05-16 [2] RSPM (R 4.4.0)
cachem 3.6.2 2023-12-11 [2] RSPM (R 4.3.0)
cli 2.4.5 2022-10-11 [2] RSPM (R 4.2.0)
devtools 0.6.35 2024-03-11 [2] RSPM (R 4.3.0)
digest 0.3.2 2021-04-29 [2] CRAN (R 4.1.1)
ellipsis 0.23 2023-11-01 [2] RSPM (R 4.3.0)
evaluate 1.2.0 2024-05-15 [2] RSPM (R 4.4.0)
fastmap 1.6.4 2024-04-25 [2] RSPM (R 4.3.0)
fs 1.7.0 2024-01-09 [2] RSPM (R 4.3.0)
glue 0.5.8.1 2024-04-04 [2] RSPM (R 4.3.0)
htmltools 1.6.4 2023-12-06 [2] RSPM (R 4.3.0)
htmlwidgets 1.6.15 2024-03-26 [2] RSPM (R 4.3.0)
httpuv * 2.0.3 2024-03-13 [1] CRAN (R 4.4.0)
igraph 1.8.8 2023-12-04 [2] RSPM (R 4.3.0)
jsonlite 1.47 2024-05-29 [2] RSPM (R 4.4.0)
knitr 1.3.2 2023-12-06 [2] RSPM (R 4.3.0)
later 1.0.4 2023-11-07 [2] RSPM (R 4.3.0)
lifecycle 2.0.3 2022-03-30 [2] RSPM (R 4.2.0)
magrittr 2.0.1 2021-11-26 [2] RSPM (R 4.2.0)
memoise 0.12 2021-09-28 [2] RSPM (R 4.2.0)
mime 0.1.1.1 2018-05-18 [2] CRAN (R 4.0.1)
miniUI 1.4.4 2024-03-17 [2] RSPM (R 4.3.0)
pkgbuild 2.0.3 2019-09-22 [2] CRAN (R 4.0.1)
pkgconfig 1.3.4 2024-01-16 [2] RSPM (R 4.3.2)
pkgload 0.3.8 2023-05-02 [2] RSPM (R 4.2.0)
profvis 1.3.0 2024-04-05 [2] RSPM (R 4.3.0)
promises 1.0.2 2023-08-10 [2] RSPM (R 4.2.0)
purrr 2.5.1 2021-08-19 [2] RSPM (R 4.2.0)
R6 1.0.12 2024-01-09 [2] RSPM (R 4.3.0)
Rcpp 2.5.0 2024-03-17 [2] RSPM (R 4.3.0)
remotes * 0.17.0 2024-06-27 [1] local
rgexf 1.1.3 2024-01-10 [2] RSPM (R 4.3.0)
rlang 2.27 2024-05-17 [2] RSPM (R 4.4.0)
rmarkdown 0.30 2024-03-23 [2] RSPM (R 4.3.0)
servr 1.2.2 2021-12-06 [2] RSPM (R 4.2.0)
sessioninfo 1.8.1.1 2024-04-02 [2] RSPM (R 4.3.0)
shiny 1.8.4 2024-05-06 [2] RSPM (R 4.4.0)
stringi 1.5.1 2023-11-14 [2] RSPM (R 4.3.0)
stringr 1.0.1 2021-11-30 [2] RSPM (R 4.2.0)
urlchecker 2.2.3 2024-02-19 [2] RSPM (R 4.3.0)
usethis 0.6.5 2023-12-01 [2] RSPM (R 4.3.0)
vctrs 0.44 2024-05-15 [2] RSPM (R 4.4.0)
xfun 3.99-0.16.1 2024-01-22 [2] RSPM (R 4.3.0)
XML 1.8-4 2019-04-21 [2] CRAN (R 4.0.1)
xtable 2.3.8 2023-12-11 [2] RSPM (R 4.3.0)
yaml
1] /usr/local/lib/R/site-library
[2] /usr/lib/R/site-library
[3] /usr/lib/R/library
[
──────────────────────────────────────────────────────────────────────────────