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Export a network to GDF format for Gephi visualization

Source: R/exportGDF.R
exportGDF.Rd

This function exports a network (unipartite or bipartite) from a data.frame to the GDF (Graph Data Format) file format, which can be directly imported into Gephi visualization software. The function handles edge data, node attributes, and color specifications.

Usage

exportGDF(
  df,
  col1 = "Node1",
  col2 = "Node2",
  weight = NULL,
  bioregions = NULL,
  bioregionalization = NULL,
  color_column = NULL,
  file = "output.gdf"
)

Arguments

df

A two- or three-column data.frame where each row represents an edge (interaction) between two nodes. The first two columns contain the node identifiers, and an optional third column can contain edge weights.

col1

A character string specifying the name of the first column in df containing node identifiers. Defaults to "Node1".

col2

A character string specifying the name of the second column in df containing node identifiers. Defaults to "Node2".

weight

A character string specifying the name of the column in df containing edge weights. If NULL (default), edges are unweighted.

bioregions

An optional bioregion.clusters object (typically from clustering functions like netclu_greedy()) or a data.frame containing bioregionalization results. When a bioregion.clusters object with colors (from bioregion_colors()) is provided, colors and bioregion assignments are automatically extracted and used for visualization. Alternatively, a data.frame with bioregionalization data can be provided, where each row represents a node with one column containing node identifiers that match those in df.

bioregionalization

A character string or a positive integer with two different uses depending on the type of bioregions:

  • When bioregions is a bioregion.clusters object with multiple partitions: specifies which partition to use. Can be either a character string with the partition name (e.g., "K_3", "K_5") or a positive integer indicating the partition index (e.g., 1 for first partition, 2 for second). If NULL (default), the first partition is used.

  • When bioregions is a data.frame: specifies the name of the column containing node identifiers that match those in df. Must be a character string. Defaults to the first column name if not specified.

color_column

A character string specifying the name of a column in bioregions containing color information in hexadecimal format (e.g., "#FF5733"). If specified, colors will be converted to RGB format for Gephi. If NULL (default), colors are automatically extracted when bioregions is a bioregion.clusters object with colors. When bioregions is a plain data.frame, this parameter must be specified to include colors.

file

A character string specifying the output file path. Defaults to "output.gdf".

Value

The function writes a GDF file to the specified path and returns nothing (NULL invisibly). The file can be directly opened in Gephi for network visualization and analysis.

Details

The GDF format is a simple text-based format used by Gephi to define graph structure. This function creates a GDF file with two main sections:

  • nodedef: Defines nodes and their attributes (name, label, and any additional bioregionalization information from bioregions)

  • edgedef: Defines edges between nodes, optionally with weights

If color_column is specified, hexadecimal color codes are automatically converted to RGB format (e.g., "#FF5733" becomes "255,87,51") as required by Gephi's color specification.

Attributes are automatically typed as VARCHAR (text), DOUBLE (numeric), or color (for color attributes).

Important note on zero-weight edges: Gephi does not handle edges with weight = 0 properly. If a weight column is specified and edges with weight = 0 are detected, they will be automatically removed from the exported network, and a warning will be issued.

Author

Boris Leroy (leroy.boris@gmail.com)
Pierre Denelle (pierre.denelle@gmail.com)
Maxime Lenormand (maxime.lenormand@inrae.fr)

Examples

# Create a simple network
net <- data.frame(
  Node1 = c("A", "A", "B", "C"),
  Node2 = c("B", "C", "C", "D"),
  Weight = c(1.5, 2.0, 1.0, 3.5)
)

# Export network with weights
if (FALSE) { # \dontrun{
exportGDF(net, weight = "Weight", file = "my_network.gdf")
} # }

# Create bioregionalization data with colors (as data.frame)
bioregion_data <- data.frame(
  node_id = c("A", "B", "C", "D"),
  cluster = c("1", "2", "3", "4"),
  node_color = c("#FF5733", "#33FF57", "#3357FF", "#FF33F5")
)

# Export network with bioregionalization and colors
if (FALSE) { # \dontrun{
exportGDF(net, 
          weight = "Weight",
          bioregions = bioregion_data,
          bioregionalization = "node_id",
          color_column = "node_color",
          file = "my_network_with_bioregions.gdf")
} # }

# Using bioregion.clusters object with colors (recommended)
if (FALSE) { # \dontrun{
data(fishmat)
net <- similarity(fishmat, metric = "Simpson")
clust <- netclu_greedy(net)
clust_colored <- bioregion_colors(clust)

# Convert to network format
net_df <- mat_to_net(fishmat, weight = TRUE)

# Export with automatic colors from clustering - very simple!
exportGDF(net_df, 
          weight = "weight",
          bioregions = clust_colored,
          file = "my_network_colored.gdf")

# With multiple partitions, specify which one to use
dissim <- similarity_to_dissimilarity(similarity(fishmat, metric = "Simpson"))
clust_hier <- hclu_hierarclust(dissim, n_clust = c(3, 5, 8))
clust_hier_colored <- bioregion_colors(clust_hier)

# Using partition name
exportGDF(net_df,
          weight = "weight",
          bioregions = clust_hier_colored,
          bioregionalization = "K_5",
          file = "my_network_K5.gdf")

# Or using partition index (2 = second partition)
exportGDF(net_df,
          weight = "weight",
          bioregions = clust_hier_colored,
          bioregionalization = 2,
          file = "my_network_partition2.gdf")
} # }