rgexf ships with an interactive graph viewer built on
top of sigma.js v3 and graphology. The widget is
zero-dependency from the user’s perspective: the required JavaScript
libraries are bundled inside the package, so no internet connection is
needed at runtime.
The main entry point is plot() — the standard R S3
method dispatches to the sigma.js widget automatically for
gexf objects. The underlying sigmajs()
function is also exported for cases where you need extra arguments such
as borderColor or explicit
width/height.
We start by building a small three-node graph from scratch.
rgexf stores visual properties (colour, position, size)
through the nodesVizAtt argument of
gexf().
library(rgexf)
# Node and edge tables
nodes <- data.frame(
id = 1:3,
label = c("Alice", "Bob", "Carol")
)
edges <- data.frame(
source = c(1L, 2L, 1L),
target = c(2L, 3L, 3L)
)
# Visual attributes
node_colors <- data.frame(
r = c(220L, 66L, 40L),
g = c( 50L, 133L, 167L),
b = c( 47L, 244L, 240L),
a = c( 1, 1, 1)
)
node_positions <- data.frame(
x = c(-1, 1, 0),
y = c( 0, 0, 1.5),
z = c( 0, 0, 0)
)
node_sizes <- c(8, 8, 8)
g <- gexf(
nodes = nodes,
edges = edges,
nodesVizAtt = list(
color = node_colors,
position = node_positions,
size = node_sizes
)
)Calling plot() on a gexf object renders the
sigma.js widget directly.
By default sigma.js renders nodes as plain filled circles — the
node’s color fills the entire disc. You can add an optional
border ring by passing borderColor (any extra arguments are
forwarded to sigmajs()):
# White border ring (15 % of the node radius)
plot(g, borderColor = "#ffffff", borderSize = 0.15)
# Dark charcoal border, slightly thicker
plot(g, borderColor = "#333333", borderSize = 0.2)The package includes a classic co-occurrence network from Victor
Hugo’s Les Misérables, originally prepared for Gephi. It
already contains viz:color, viz:position, and
viz:size attributes, so the widget picks them up
automatically.
lesmi_path <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
lesmi <- read.gexf(lesmi_path)
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>
#> <node id="58" label="Enjolras">
#> <attvalues>
#> <attvalue for="modularity_class" value="8"/>
#> </attvalues>
#> <viz:size value="42.4"/>
#> <viz:position x="355.78366" y="74.882454"/>
#> <viz:color r="91" g="245" b="91"/>
#> </node>
#> <node id="62" label="Courfeyrac">
#> <attvalues>
#> <attvalue for="modularity_class" value="8"/>
#> </attvalues>
#> <viz:size value="36.91429"/>
#> <viz:position x="436.17184" y="12.7286825"/>
#> <viz:color r="91" g="245" b="91"/>
#> </node>
#> <node id="64" label="Bossuet">
#> <attvalues>
#> <attvalue for="modularity_class" value="8"/>
#> </attvalues>
#> <viz:size value="36.91429"/>
#> <viz:position x="455.81955" y="115.45826"/>
#> <viz:color r="91" g="245" b="91"/>
#> </node>
#> <node id="63" label="Bahorel">
#> <attvalues>
#> <attvalue for="modularity_class" value="8"/>
#> </attvalues>
#> <viz:size value="34.17143"/>
#> <viz:position x="602.55225" y="-16.421427"/>
#> <viz:color r="91" g="245" b="91"/>
#> </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"/>
#> <edge id="6" source="6" target="0"/>
#> <edge id="7" source="7" target="0"/>
#> <edge id="8" source="8" target="0" weight="2.0"/>
#> <edge id="9" source="9" target="0"/>
#> ...
#> </edges>
#> </graph>
#> </gexf>The colours come directly from the GEXF file. Each character group is assigned a distinct hue by the original dataset, so the community structure is immediately visible.
The default rendering is sigma.js’s plain filled circle. If you want
to separate overlapping nodes or simply add visual polish, pass a
borderColor. A white outer ring works well on light
backgrounds:
The borderColor argument accepts any CSS colour string
("#rrggbb", "rgb(r,g,b)", named colours such
as "white", etc.). The borderSize argument is
a number between 0 and 1 representing the border width as a fraction of
the node’s radius — 0.15 means the ring takes up 15 % of
the node radius.
For a dark-themed background, try a darker value:
The older gexf-js-based viewer is preserved as
plot_gexfjs() for users who need the file-server
workflow:
#> GEXF graph successfully written at:
#> /tmp/RtmpHntBBy/network.gexfplot_gexfjs() copies the gexf-js viewer files together
with the graph to a directory (tempdir() by default). When
called interactively with the default copy.only = FALSE, it
also starts a local HTTP server via servr::httd() and opens
the graph in the default browser – useful for standalone HTML reports or
for users who prefer the original gexf-js interface. In non-interactive
sessions (such as when this vignette is built) only the files are
copied. You can also embed the graph in a Shiny app or R Markdown using
the gexfjs() function:
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04 LTS
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#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
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#>
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#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] rgexf_0.17.0 rmarkdown_2.31
#>
#> loaded via a namespace (and not attached):
#> [1] cli_3.6.6 knitr_1.51 rlang_1.3.0 xfun_0.60
#> [5] otel_0.2.0 promises_1.5.0 jsonlite_2.0.0 buildtools_1.0.0
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#> [17] fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5 compiler_4.6.1
#> [21] igraph_2.3.3 Rcpp_1.1.2 htmlwidgets_1.6.4 pkgconfig_2.0.3
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