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.
-
We now have a hex sticker!
-
Users can now cite properly
rgexfwith JOSS (seecitation(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 thenfirst nodes/edges.
-
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.igraphcorrectly processes edge attributes (#38 reported by @balachia). -
Time range is now correctly computed (#19).
-
Non-integer ids were incorrectly processed when reading GEXF files.
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")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)'.
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.
# 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>
##
# 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>
##
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>
##
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 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
##
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## callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
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## desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0)
## devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0)
## digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
## fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
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## igraph * 1.2.6 2020-10-06 [1] CRAN (R 4.1.0)
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## rgexf * 0.16.2 2021-08-12 [1] local
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## [2] /usr/local/lib/R/site-library
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