Getting started with rgexf
Introduction
The rgexf package provides a way to interact with GEXF files. The GEXF standard was
developed by the Gephi–“Like Photoshop
for graphs”–core team, and can be used to save static and dynamic
networks.
With the rgexf package, users can create
gexf (R) objects from scratch, import GEXF files, coerce
gexf objects into igraph objects, and
visualize graphs using the gexf-js JavaScript
library. In this vignette, we will illustrate how can we (a) import
a GEXF file into R and visualize it with igraph, and (b)
create a gexf object from scratch.
Reading GEXF files
The rgexf package comes with a network from Les
Misérables, which is featured in Gephi. To read GEXF files, we can use
the read.gexf function:
# Loading rgexf
library(rgexf)
# Accessing the path of the file
fn <- system.file(
"gexf-graphs/lesmiserables.gexf", package = "rgexf"
)
lesmi <- read.gexf(fn)
# Taking a look at the first handful of nodes and edges
head(lesmi)## <?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 directly plot the graph using the
plot.gexf method–through the gexf-js
library–or coercing it into an igraph object and use
igraph’s plotting engine:
## IGRAPH eb332a6 UNW- 77 254 --
## + attr: layout (g/n), name (v/c), color (v/c), size (v/n), weight (e/n)
## + edges from eb332a6 (vertex names):
## [1] Myriel --Napoleon Myriel --MlleBaptistine
## [3] Myriel --MmeMagloire MlleBaptistine--MmeMagloire
## [5] Myriel --CountessDeLo Myriel --Geborand
## [7] Myriel --Champtercier Myriel --Cravatte
## [9] Myriel --Count Myriel --OldMan
## [11] Myriel --Valjean Valjean --MlleBaptistine
## [13] Valjean --MmeMagloire Labarre --Valjean
## [15] Valjean --Marguerite Valjean --MmeDeR
## + ... omitted several edges
We can also go back:
## <?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="2024-11-18">
## <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="Myriel" label="Myriel">
## <viz:color r="91" g="91" b="245" a="1"/>
## <viz:position x="-148.379397464743" y="-140.395409747888" z="0"/>
## <viz:size value="1.86270876623377"/>
## </node>
## <node id="Napoleon" label="Napoleon">
## <viz:color r="91" g="91" b="245" a="1"/>
## <viz:position x="-209.928377825858" y="-212.835089666009" z="0"/>
## <viz:size value="0.25974025974026"/>
## </node>
## <node id="Labarre" label="Labarre">
## <viz:color r="245" g="91" b="91" a="1"/>
## <viz:position x="-76.1564912097887" y="-108.343126644676" z="0"/>
## <viz:size value="0.25974025974026"/>
## </node>
## <node id="Valjean" label="Valjean">
## <viz:color r="245" g="91" b="91" a="1"/>
## <viz:position x="-75.5824164344556" y="10.4450055312959" z="0"/>
## <viz:size value="6.49350649350649"/>
## </node>
## <node id="Marguerite" label="Marguerite">
## <viz:color r="245" g="91" b="91" a="1"/>
## <viz:position x="-178.064757789707" y="97.9855519958049" z="0"/>
## <viz:size value="0.437847987012987"/>
## </node>
## <node id="MmeDeR" label="MmeDeR">
## <viz:color r="245" g="91" b="91" a="1"/>
## <viz:position x="-118.871735089594" y="-80.7795279631479" z="0"/>
## <viz:size value="0.25974025974026"/>
## </node>
## ...
## </nodes>
## <edges>
## <edge id="0" source="Myriel" target="Napoleon" weight="1"/>
## <edge id="1" source="Myriel" target="MlleBaptistine" weight="8"/>
## <edge id="2" source="Myriel" target="MmeMagloire" weight="10"/>
## <edge id="3" source="MlleBaptistine" target="MmeMagloire" weight="6"/>
## <edge id="4" source="Myriel" target="CountessDeLo" weight="1"/>
## <edge id="5" source="Myriel" target="Geborand" weight="1"/>
## ...
## </edges>
## </graph>
## </gexf>Using the plot.gexf method–which uses the
gexf-js JavaScript library–results in a Web visualization
of the graph, like this:
An live version of the figure is available here.
Creating GEXF files
This example was extracted directly from the demo “gexfrandom.” Here we create three networks with the same set of vertices and layout, we color them and finalize plotting it with igraph.
Creating the vertices:
# Vertex
n <- 30
prb <- .3
vertex1 <- data.frame(id = 1:n, label = 1:n)
vertex2 <- data.frame(id = (n + 1):(2 * n), label = (n + 1):(2 * n))
vertex3 <- data.frame(
id = (2 * n + 1):(3 * n), label = (2 * n + 1):(3 * n)
)Building edges:
# Edges
edges1 <- combn(vertex1$label, 2)
edges1 <- edges1[, which(runif(ncol(edges1)) > (1 - prb))]
edges1 <- data.frame(source = edges1[1, ], target = edges1[2, ])
edges2 <- combn(vertex2$label, 2)
edges2 <- edges2[, which(runif(ncol(edges2)) > (1 - prb))]
edges2 <- data.frame(source = edges2[1, ], target = edges2[2, ])
edges3 <- combn(vertex3$label, 2)
edges3 <- edges3[, which(runif(ncol(edges3)) > (1 - prb))]
edges3 <- data.frame(source = edges3[1, ], target = edges3[2, ])We can and add visual attributes:
# Visual attributes
size <- runif(n, max = 100)
color <- terrain.colors(n)
color <- color[order(runif(n))][1:n]
color <- cbind(t(col2rgb(color)), 1)
color2 <- heat.colors(n)
color2 <- color2[order(runif(n))][1:n]
color2 <- cbind(t(col2rgb(color2)), 1)
color3 <- topo.colors(n)
color3 <- color3[order(runif(n))][1:n]
color3 <- cbind(t(col2rgb(color3)), 1)Generating a layout:
# Nice layout
pos <- matrix(0, nrow = n, ncol = 3)
for (i in 2:n) {
pos[i, 1] <- pos[i - 1, 1] + cos(2 * pi * (i * 1.7 - 1) / n)
pos[i, 2] <- pos[i - 1, 2] + sin(2 * pi * (i - 1) / n)
}
pos <- pos / (max(pos) - min(pos))
pos2 <- pos
pos2[, 1] <- pos2[, 1] + max(pos2[, 1]) - min(pos[, 1])
pos3 <- pos
pos3[, 1] <- pos3[, 1] + max(pos2[, 1]) - min(pos[, 1])And finally, we can build the gexf object:
graph <- gexf(
rbind(vertex1, vertex2, vertex3),
rbind(edges1, edges2, edges3),
nodesVizAtt = list(
size = c(size, size, size),
color = rbind(color, color2, color3),
position = rbind(pos, pos2, pos3)
)
)
# Taking a quick look
head(graph)## <?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="2024-11-18">
## <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="1">
## <viz:color r="233" g="187" b="62" a="1"/>
## <viz:position x="-140.199919726949" y="-250" z="0"/>
## <viz:size value="5.55555555555556"/>
## </node>
## <node id="2" label="2">
## <viz:color r="235" g="178" b="94" a="1"/>
## <viz:position x="-114.232657063944" y="-239.073800366903" z="0"/>
## <viz:size value="2.75415710515231"/>
## </node>
## <node id="3" label="3">
## <viz:color r="242" g="242" b="242" a="1"/>
## <viz:position x="-94.8700927475552" y="-217.698928454398" z="0"/>
## <viz:size value="0.187776451016345"/>
## </node>
## <node id="4" label="4">
## <viz:color r="240" g="201" b="192" a="1"/>
## <viz:position x="-84.540989802301" y="-186.809568733076" z="0"/>
## <viz:size value="3.05941177828193"/>
## </node>
## <node id="5" label="5">
## <viz:color r="151" g="211" b="0" a="1"/>
## <viz:position x="-84.540989802301" y="-147.755734446353" z="0"/>
## <viz:size value="1.90801670817263"/>
## </node>
## <node id="6" label="6">
## <viz:color r="232" g="195" b="46" a="1"/>
## <viz:position x="-94.8700927475552" y="-102.244265553647" z="0"/>
## <viz:size value="0.381918795494298"/>
## </node>
## ...
## </nodes>
## <edges>
## <edge id="0" source="1" target="7" weight="1"/>
## <edge id="1" source="1" target="10" weight="1"/>
## <edge id="2" source="1" target="14" weight="1"/>
## <edge id="3" source="1" target="15" weight="1"/>
## <edge id="4" source="1" target="16" weight="1"/>
## <edge id="5" source="2" target="8" weight="1"/>
## ...
## </edges>
## </graph>
## </gexf>As before, we can either directly call the plot function for
gexf objects, or coerce it into an igraph
object:
