Package 'rgexf'

Description

Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others).

Details

Using the XML package, it allows the user to easily build/read graph files including attributes, GEXF viz attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting.

Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through "gexf-js" (a javascript library) and interact with the igraph package.

Finally, the functions igraph.to.gexf and gexf.to.igraph convert objects from igraph to gexf and viceversa keeping attributes and colors.

Please visit the project home for more information: https://github.com/gvegayon/rgexf.

Note

See the GEXF primer for details on the GEXF graph format: http://gexf.net/1.2draft/gexf-12draft-primer.pdf

Author(s)

Maintainer: George Vega Yon [email protected] (ORCID)

Authors:

• George Vega Yon [email protected] (ORCID)

Other contributors:

• Jorge Fábrega Lacoa [contributor]

• Joshua Kunst [contributor]

• Raphaël Velt (gexf-js library) [copyright holder]

• Gephi Consortium (GEXF language) [copyright holder]

• Cornelius Fritz (what: JOSS reviewer) [reviewer]

• Jonathan Cardoso Silva (what: JOSS reviewer) [reviewer]

References

• rgexf project site: https://github.com/gvegayon/rgexf

• Gephi project site: https://gephi.org/

• GEXF project site: https://gexf.net/

• gexf-js project website: https://github.com/raphv/gexf-js

• Sigmasj project site: https://www.sigmajs.org/

See Also

Useful links:

• https://gvegayon.github.io/rgexf/

• Report bugs at https://github.com/gvegayon/rgexf/issues

Examples

if (interactive()) {
    demo(gexf) # Example of gexf command using fictional data.
    demo(gexfattributes) # Working with attributes.
    demo(gexfbasic) # Basic net.
    demo(gexfdynamic) # Dynamic net.
    demo(edge.list) # Working with edges lists.
    demo(gexffull) # All the package.
    demo(gexftwitter) # Example with real data of chilean twitter accounts.
    demo(gexfdynamicandatt) # Dynamic net with static attributes.
    demo(gexfbuildfromscratch) # Example building a net from scratch.
    demo(gexfigraph) # Two-way gexf-igraph conversion
    demo(gexfrandom) # A nice routine creating a good looking graph
}

Description

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

Usage

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

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).

Value

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

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.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

References

The GEXF project website: https://gexf.net/

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

Description

Looks for duplicated edges and reports the number of instances of them.

Usage

check.dpl.edges(edges, undirected = FALSE, order.edgelist = TRUE)

Arguments

Details

check.dpl.edges looks for duplicated edges reporting duplicates and counting how many times each edge is duplicated.

For every group of duplicated edges only one will be accounted to report number of instances (which will be recognized with a value higher than 2 in the reps column), the other ones will be assigned an NA at the reps value.

Value

A three column data.frame with colnames “source”, “target” “reps”.

Author(s)

George Vega Yon

See Also

Other manipulation: switch.edges()

Examples

# An edgelist with duplicated dyads
  relations <- cbind(c(1,1,3,3,4,2,5,6), c(2,3,1,1,2,4,1,1))
  
  # Checking duplicated edges (undirected graph)
  check.dpl.edges(edges=relations, undirected=TRUE)

Description

Checks time

Usage

checkTimes(x, format = "date")

Arguments

Value

Logical.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

Examples

test <- c("2012-01-17T03:46:41", "2012-01-17T03:46:410")
  checkTimes(test, format="dateTime")
  checkTimes("2012-02-01T00:00:00", "dateTime")

Description

Generates two data frames (nodes and edges) from a list of edges

Usage

edge.list(x)

Arguments

Details

edge.list transforms the input into a two-elements list containing a dataframe of nodes (with columns “id” and “label”) and a dataframe of edges. The last one is numeric (with columns “source” and “target”) and based on auto-generated nodes' ids.

Value

A list containing two data frames.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

Examples

edgelist <- matrix(
    c("matthew","john",
      "max","stephen",
      "matthew","stephen"),
    byrow=TRUE, ncol=2)
  
  edge.list(edgelist)

Description

Sample of accounts by December 2011.

Format

A data frame containing 6065 observations.

Source

Fabrega and Paredes (2012): “La politica en 140 caracteres” en Intermedios: medios de comunicacion y democracia en Chile. Ediciones UDP

Description

Uses the gexf-js JavaScript viewer by copying static files to a directory and optionally launching a local web server via the servr package. For the modern htmlwidget-based renderer, use plot.gexf or sigmajs.

Usage

gexf_js_config(
  dir,
  graphFile = "network.gexf",
  showEdges = TRUE,
  useLens = FALSE,
  zoomLevel = 0,
  curvedEdges = TRUE,
  edgeWidthFactor = 1,
  minEdgeWidth = 1,
  maxEdgeWidth = 50,
  textDisplayThreshold = 9,
  nodeSizeFactor = 1,
  replaceUrls = TRUE,
  showEdgeWeight = TRUE,
  showEdgeLabel = TRUE,
  sortNodeAttributes = TRUE,
  showId = TRUE,
  showEdgeArrow = TRUE,
  language = FALSE
)

plot_gexfjs(
  x,
  graphFile = "network.gexf",
  dir = tempdir(),
  overwrite = TRUE,
  httd.args = list(),
  copy.only = FALSE,
  ...
)

Arguments

Details

Currently, the only languages supported are: German (de), English (en), French (fr), Spanish (es), Italian (it), Finnish (fi), Turkish (tr), Greek (el), Dutch (nl)

The server is launched only when interactive() == TRUE and copy.only == FALSE.

References

gexf-js project website https://github.com/raphv/gexf-js.

Examples

if (interactive()) {
  path <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
  graph <- read.gexf(path)
  plot_gexfjs(graph)
}

Description

Takes a node matrix (or dataframe) and an edge matrix (or dataframe) and creates a gexf object containing a data-frame representation and a gexf representation of a graph.

Usage

gexf(
  nodes,
  edges,
  edgesLabel = NULL,
  edgesId = NULL,
  edgesAtt = NULL,
  edgesWeight = NULL,
  edgesVizAtt = list(color = NULL, size = NULL, shape = NULL),
  nodesAtt = NULL,
  nodesVizAtt = list(color = NULL, position = NULL, size = NULL, shape = NULL, image =
    NULL),
  nodeDynamic = NULL,
  edgeDynamic = NULL,
  digits = getOption("digits"),
  output = NA,
  tFormat = "double",
  defaultedgetype = "undirected",
  meta = list(creator = "NodosChile", description =
    "A GEXF file written in R with \"rgexf\"", keywords =
    "GEXF, NodosChile, R, rgexf, Gephi"),
  keepFactors = FALSE,
  encoding = "UTF-8",
  vers = "1.3",
  rescale.node.size = TRUE,
  relsize = max(0.01, 1/nrow(nodes)),
  radius = 500
)

write.gexf(nodes, ...)

Arguments

Details

Just like nodesVizAtt and edgesVizAtt, nodesAtt and edgesAtt must have the same number of rows as nodes and edges, respectively. Using data frames is necessary as in this way data types are preserved.

nodesVizAtt and edgesVizAtt allow using visual attributes such as color, position (nodes only), size (nodes only), thickness (edges only) shape and image (nodes only).

• Color is defined by the RGBA color model, thus for every node/edge the color should be specified through a data-frame with columns r (red), g (green), b (blue) with integers between 0 and 256 and a last column with alpha values as a float between 0.0 and 1.0.

• Position, for every node, it is a three-column data-frame including x, y and z coordinates. The three components must be float.

• Size as a numeric colvector (float values).

• Thickness (see size).

• Node Shape (string), currently unsupported by Gephi, can take the values of disk, square, triangle, diamond and image.

• Edge Shape (string), currently unsupported by Gephi, can take the values of solid, dotted, dashed and double.

• Image (string), currently unsupported by Gephi, consists on a vector of strings representing URIs.

nodeDynamic and edgeDynamic allow to draw dynamic graphs. It should contain two columns start and end, both allowing NA value. It can be use jointly with tFormat which by default is set as “double”. Currently accepted time formats are:

• Integer or double.

• International standard date yyyy-mm-dd.

• dateTime W3 XSD (http://www.w3.org/TR/xmlschema-2/#dateTime).

NA values in the first column are filled with the min of c(nodeDynamic, edgeDynamic), whereas if in the second column is replaces with the max.

More complex time sequences like present/absent nodes and edges can be added with add.node.spell and add.edge.spell respectively.

Value

A gexf class object (list). Contains the following:

• meta : (list) Meta data describing the graph.

• mode : (list) Sets the default edge type and the graph mode.

• atts.definitions: (list) Two data-frames describing nodes and edges attributes.

• nodesVizAtt : (data-frame) A multi-column data-frame with the nodes' visual attributes.

• edgesVizAtt : (data-frame) A multi-column data-frame with the edges' visual attributes.

• nodes : (data-frame) A two-column data-frame with nodes' ids and labels.

• edges : (data-frame) A five-column data-frame with edges' ids, labels, sources, targets and weights.

• graph : (String) GEXF (XML) representation of the graph.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

References

The GEXF project website: https://gexf.net/

See Also

new.gexf.graph()

Examples

if (interactive()) {
  demo(gexf) # Example of gexf command using fictional data.
  demo(gexfattributes) # Working with attributes.
  demo(gexfbasic) # Basic net.
  demo(gexfdynamic) # Dynamic net.
  demo(edge.list) # Working with edges lists.
  demo(gexffull) # All the package.
  demo(gexftwitter) # Example with real data of chilean twitter accounts.
  demo(gexfdynamicandatt) # Dynamic net with static attributes.
  demo(gexfbuildfromscratch) # Example building a net from scratch.
  demo(gexfrandom)
}

Description

Methods to print and summarize gexf class objects

Usage

## S3 method for class 'gexf'
print(x, file = NA, replace = F, nnodes = 10, nedges = 10, ...)

## S3 method for class 'gexf'
summary(object, ...)

Arguments

Details

print.gexf displays the graph (XML) in the console. If file is not NA, a GEXF file will be exported to the indicated filepath.

summay.gexf prints summary statistics and information about the graph.

Value

Author(s)

George G. Vega Yon

Joshua B. Kunst

See Also

See also write.gexf, plot.gexf

Examples

if (interactive()) {
    # Data frame of nodes
    people <- data.frame(id=1:4, label=c("juan", "pedro", "matthew", "carlos"),
                     stringsAsFactors=F)
    
    # Data frame of edges
    relations <- data.frame(source=c(1,1,1,2,3,4,2,4,4), 
                        target=c(4,2,3,3,4,2,4,1,1))
    
    # Building gexf graph
    mygraph <- gexf(nodes=people, edges=relations)
    
    # Summary and pring
    summary(mygraph)
    
    write.gexf(mygraph, output="mygraph.gexf", replace=TRUE)
    
    # Plotting
    plot(mygraph)
    
  }

Description

Creates an htmlwidget that renders a GEXF file using the bundled gexf-js library.

Usage

gexfjs(
  gexf = system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf"),
  width = "100%",
  height = "400px"
)

gexfjsOutput(outputId, width = "100%", height = "400px")

renderGexfjs(expr, env = parent.frame(), quoted = FALSE)

Arguments

Value

An htmlwidget object.

Description

List the first n_nodes and n_edges of the gexf file.

Usage

## S3 method for class 'gexf'
head(x, n_nodes = 6L, n_edges = n_nodes, ...)

Arguments

Examples

fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
g  <- read.gexf(fn)
head(g, n_nodes = 5)

Description

Converts objects between gexf and igraph objects keeping attributes, edge weights and colors.

Usage

igraph.to.gexf(igraph.obj, ...)

gexf.to.igraph(gexf.obj)

Arguments

Details

If the position argument is not NULL, the new gexf object will include the position viz-attribute.

Value

• For igraph.to.gexf : gexf class object

• For gexf.to.igraph : igraph class object

Author(s)

George Vega Yon [email protected]

See Also

layout()

Examples

if (interactive()) {
  # Running demo
  demo(gexfigraph)
}
 
  fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
  gexf1 <- read.gexf(fn)
  igraph1 <- gexf.to.igraph(gexf1)
  gexf2 <- igraph.to.gexf(igraph1)
  
if (interactive()) {
  # Now, let's do it with a layout! (although we can just use
  # the one that comes with lesmiserables :))
  pos <- igraph::layout_nicely(igraph1)
  plot(
    igraph.to.gexf(igraph1, nodesVizAtt = list(position=cbind(pos, 0))),
    edgeWidthFactor = .01)
 }

Description

Builds an empty gexf object containing all the class's attributes.

Usage

new.gexf.graph(
  defaultedgetype = "undirected",
  meta = list(creator = "NodosChile", description =
    "A graph file writing in R using 'rgexf'", keywords =
    "gexf graph, NodosChile, R, rgexf")
)

Arguments

Value

A gexf object.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

References

The GEXF project website: https://gexf.net/

Examples

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

Description

plot.gexf renders a gexf object as an interactive sigma.js htmlwidget. For the legacy gexf-js file-server approach, use plot_gexfjs.

Usage

## S3 method for class 'gexf'
plot(x, y = NULL, width = NULL, height = NULL, ...)

Arguments

Details

plot.gexf delegates to sigmajs, which produces an htmlwidget powered by sigma.js. Node positions, colours, and sizes are read directly from the GEXF ⁠viz:*⁠ attributes, so the graph must contain them. If they are absent you can round-trip through igraph:

x <- igraph.to.gexf(gexf.to.igraph(x))
plot(x)

See Also

sigmajs(), plot_gexfjs()

Examples

if (interactive()) {
  path <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
  graph <- read.gexf(path)
  plot(graph)
}

Description

read.gexf reads gexf graph files and imports its elements as a gexf class object

Usage

read.gexf(x)

Arguments

Value

A gexf object.

Note

By the time attributes and viz-attributes aren't supported.

Author(s)

George Vega Yon

Jorge Fabrega Lacoa

References

The GEXF project website: https://gexf.net/

Examples

fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
  mygraph <- read.gexf(fn)

Description

Creates an htmlwidget that renders a GEXF graph using sigma.js v3 and graphology. Node positions, colours, and sizes are read from the ⁠viz:*⁠ attributes embedded in the GEXF document. Nodes are drawn with a thin border ring whose colour is controlled by borderColor.

Usage

sigmajs(
  gexf = system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf"),
  width = NULL,
  height = NULL,
  borderColor = NULL,
  borderSize = 0.15
)

sigmajsOutput(outputId, width = "100%", height = "400px")

renderSigmajs(expr, env = parent.frame(), quoted = FALSE)

Arguments

Value

An htmlwidget object.

Examples

if (interactive()) {
  path <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
  sigmajs(path)

  # White border ring
  sigmajs(path, borderColor = "#ffffff", borderSize = 0.15)
}

Description

Puts the lowest id node among every dyad as source (and the other as target)

Usage

switch.edges(edges)

Arguments

Details

edge.list transforms the input into a two-elements list containing a dataframe of nodes (with columns “id” and “label”) and a dataframe of edges. The last one is numeric (with columns “source” and “target”) and based on auto-generated nodes' ids.

Value

A list containing two data frames.

Author(s)

George Vega Yon

See Also

Other manipulation: check.dpl.edges()

Examples

relations <- cbind(c(1,1,3,4,2,5,6), c(2,3,1,2,4,1,1))
  relations
  
  switch.edges(relations)

Description

Sample of accounts by December 2011.

Format

A data frame containing 148 observations.

Source

Fabrega and Paredes (2012): “La politica en 140 caracteres” en Intermedios: medios de comunicacion y democracia en Chile. Ediciones UDP