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Convert to Cograph Network

Source: R/class-network.R
as_cograph.Rd

Creates a lightweight cograph_network object from various network inputs. The resulting object is a named list with all data accessible via $.

Usage

as_cograph(x, directed = NULL, simplify = FALSE, ...)

to_cograph(x, directed = NULL, ...)

Arguments

x

Network input. Can be:

  • A square numeric matrix (adjacency/weight matrix)

  • A data frame with edge list (from, to, optional weight columns)

  • An igraph object

  • A statnet network object

  • A qgraph object

  • A tna object

  • An existing cograph_network object (returned as-is)

directed

Logical. Force directed interpretation. NULL for auto-detect.

simplify

Logical or character. If FALSE (default), every transition from tna sequence data is a separate edge. If TRUE or a string ("sum", "mean", "max", "min"), duplicate edges are aggregated.

...

Additional arguments (currently unused).

Value

A cograph_network object: a named list with components:

nodes

Data frame with id, label, and optional layout or metadata columns

edges

Data frame with from, to, weight columns

directed

Logical indicating if network is directed

weights

Full n×n weight matrix when available for matrix/TNA round-trips, or NULL

data

Original estimation data (sequence matrix, edge list, etc.), or NULL

meta

Consolidated metadata list with sub-fields: source (input type string), layout (layout info list or NULL), tna (TNA metadata or NULL), and optionally splot (producer-supplied rendering hints read by splot)

node_groups

Optional node groupings data frame

A cograph_network object. See as_cograph.

Details

The cograph_network format is designed to be:

  • Lean: Only essential data stored, computed values derived on demand

  • Modern: Uses named list elements instead of attributes for clean $ access

  • Compatible: Works seamlessly with splot() and other cograph functions

Producer packages may attach optional plotting hints under meta$splot. The recognized fields are renderer (which cograph renderer to use), weight (the edge column or matrix to render as weight), and defaults (a named list of renderer arguments). Entries in defaults are defaults only — user-supplied arguments to splot always override them. renderer and weight define which view is rendered and are not overridden by plot arguments.

Use getter functions for programmatic access: get_nodes, get_edges, get_labels, n_nodes, n_edges

Use setter functions to modify: set_nodes, set_edges, set_layout

See also

get_nodes to extract the nodes data frame, get_edges to extract edges as a data frame, n_nodes and n_edges for counts, is_directed to check directedness, splot for plotting

Examples

mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
net <- as_cograph(mat)
get_nodes(net)
#>   id label name  x  y
#> 1  1     1    1 NA NA
#> 2  2     2    2 NA NA
#> 3  3     3    3 NA NA
get_edges(net)
#>   from to weight
#> 1    1  2      1
#> 2    1  3      1
#> 3    2  3      1
splot(net)

mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
net <- to_cograph(mat)