Adding and removing nodes/edges from gexf objects

Manipulates gexf objects adding and removing nodes and edges from both, its dataframe representation and its XML representation.

add.gexf.node(
  graph,
  id = NA,
  label = NA,
  start = NULL,
  end = NULL,
  vizAtt = list(color = NULL, position = NULL, size = NULL, shape = NULL, image = NULL),
  atts = NULL
)

add.gexf.edge(
  graph,
  source,
  target,
  id = NULL,
  type = NULL,
  label = NULL,
  start = NULL,
  end = NULL,
  weight = 1,
  vizAtt = list(color = NULL, thickness = NULL, shape = NULL),
  atts = NULL,
  digits = getOption("digits")
)

rm.gexf.node(graph, id = NULL, number = NULL, rm.edges = TRUE)

rm.gexf.edge(graph, id = NULL, number = NULL)

add.node.spell(
  graph,
  id = NULL,
  number = NULL,
  start = NULL,
  end = NULL,
  digits = getOption("digits")
)

add.edge.spell(
  graph,
  id = NULL,
  number = NULL,
  start = NULL,
  end = NULL,
  digits = getOption("digits")
)

Arguments

graph	A gexf-class object.
id	A node/edge id (normally numeric value).
label	A node/edge label.
start	Starting time period
end	Ending time period
vizAtt	A list of node/edge viz attributes (see write.gexf()).
atts	List of attributes, currently ignored.
source	Source node's id.
target	Target node's id.
type	Type of connection (edge).
weight	Edge weight.
digits	Integer. Number of decimals to keep for nodes/edges sizes. See print.default()
number	Index number(s) of a single or a group of nodes or edges.
rm.edges	Whether to remove or not existing edges.

Value

A gexf object (see write.gexf()).

Details

new.gexf.graph Creates a new gexf empty object (0 nodes 0 edges).

add.gexf.node and add.gexf.edge allow adding nodes and edges to a gexf object (graph) one at a time. rm.gexf.node and rm.gexf.edges remove nodes and edges respectively.

In the case of rm.gexf.node, by default every edge linked to the node that is been removed will also be removed (rm.edges = TRUE).

Spells

While the start and end attributes can be included in nodes and edges, spells provide a way to represent presence and absence of elements throughout time.

We can use spells to indicate windows during which the element is present or not. For example, a node that shows up from time 1 to time two and re-appears after time four can have two spells:

<spell start="1.0" end="2.0">
<spell start="4.0">

In the case of the functions add.edge.spell and add.node.spell, edges and nodes to which you want to add spells should already exist.

References

The GEXF project website: https://gephi.org/gexf/format/

Author

George Vega Yon

Jorge Fabrega Lacoa

Examples

if (interactive()) {
  demo(gexfbuildfromscratch)
}

# Creating spells ------------------------------------------------------
g <- new.gexf.graph()

# Adding a few nodes + edges
g <- add.gexf.node(g, id = 0, label = "A")
g <- add.gexf.node(g, id = 1, label = "B")
g <- add.gexf.node(g, id = 2, label = "C")

g <- add.gexf.edge(g, source = 0, target = 1)
g <- add.gexf.edge(g, source = 0, target = 2)

# Now we add spells:
# - Node 0: 1.0 -> 2.0, 3.0 -> Inf
# - edge 1: 1.0 -> 2.0, 3.5 -> Inf
g <- add.node.spell(g, 0, start = 1, end = 2)
g <- add.node.spell(g, 0, start = 3)

g <- add.edge.spell(g, 1, start = 1, end = 2)
g <- add.edge.spell(g, 1, start = 3.5)

g
#> <?xml version="1.0"?>
#> <gexf schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
#>  <meta lastmodifieddate="2023-05-26">
#>   <creator>NodosChile</creator>
#>   <description>A graph file writing in R using &apos;rgexf&apos;</description>
#>   <keywords>gexf graph, NodosChile, R, rgexf</keywords>
#>  </meta>
#>  <graph mode="static">
#>   <nodes>
#>    <node id="0" label="A">
#>     <spells>
#>      <spell start="1" end="2"/>
#>      <spell start="3"/>
#>     </spells>
#>    </node>
#>    <node id="1" label="B"/>
#>    <node id="2" label="C"/>
#>   </nodes>
#>   <edges>
#>    <edge id="1" source="0" target="1" weight="1">
#>     <spells>
#>      <spell start="1" end="2"/>
#>      <spell start="3.5"/>
#>     </spells>
#>    </edge>
#>    <edge id="2" source="0" target="2" weight="1"/>
#>   </edges>
#>  </graph>
#> </gexf>