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CographNetwork R6 Class

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

Core class representing a network for visualization. Stores nodes, edges, layout coordinates, and aesthetic mappings.

Value

A CographNetwork R6 object.

Active bindings

n_nodes

Number of nodes in the network.

n_edges

Number of edges in the network.

is_directed

Whether the network is directed.

has_weights

TRUE when any edge weight differs from 1.

node_labels

Vector of node labels, taken from the labels column of the node table when present and from label otherwise.

Methods

Public methods

Method new()

Create a new CographNetwork object.

Usage

CographNetwork$new(
  input = NULL,
  directed = NULL,
  nodes = NULL,
  simplify = FALSE
)

Arguments

input

Network input, such as a matrix, edge list, igraph, statnet network, qgraph or tna object. NULL creates an empty object.

directed

Logical. Forces a directed or undirected interpretation. NULL detects it from the input.

nodes

NULL or a data frame of node attributes. Its rows are matched to the node labels by a name, label or id column, tried in that order, and the remaining columns are added to the node table. When no column matches and the row count equals the number of nodes, the columns are added in row order. A labels column supplies the display labels returned by $node_labels.

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 transitions are aggregated. Other inputs are not affected.

Returns

A new CographNetwork object.

Method clone_network()

Create a copy with the same nodes, edges, weights, layout, aesthetics, theme, layout information and plot parameters.

Usage

CographNetwork$clone_network()

Returns

A new CographNetwork object.

Method set_nodes()

Set nodes data frame.

Usage

CographNetwork$set_nodes(nodes)

Arguments

nodes

Data frame with node information.

Returns

The object itself, invisibly.

Method set_edges()

Set edges data frame.

Usage

CographNetwork$set_edges(edges)

Arguments

edges

Data frame with edge information.

Returns

The object itself, invisibly.

Method set_directed()

Set directed flag.

Usage

CographNetwork$set_directed(directed)

Arguments

directed

Logical.

Returns

The object itself, invisibly.

Method set_weights()

Set edge weights.

Usage

CographNetwork$set_weights(weights)

Arguments

weights

Numeric vector of edge weights, one per edge.

Returns

The object itself, invisibly.

Method set_layout_coords()

Set layout coordinates.

Usage

CographNetwork$set_layout_coords(coords)

Arguments

coords

Matrix or data frame with at least two columns and one row per node. The first two columns are renamed x and y and are also written to the node table. NULL leaves the layout unchanged.

Returns

The object itself, invisibly.

Method set_node_aes()

Set node aesthetics. The list is merged into the current node aesthetics.

Usage

CographNetwork$set_node_aes(aes)

Arguments

aes

Named list of aesthetic parameters.

Returns

The object itself, invisibly.

Method set_edge_aes()

Set edge aesthetics. The list is merged into the current edge aesthetics.

Usage

CographNetwork$set_edge_aes(aes)

Arguments

aes

Named list of aesthetic parameters.

Returns

The object itself, invisibly.

Method set_theme()

Set theme.

Usage

CographNetwork$set_theme(theme)

Arguments

theme

CographTheme object or theme name.

Returns

The object itself, invisibly.

Method get_nodes()

Get nodes data frame.

Usage

CographNetwork$get_nodes()

Returns

Data frame with node information.

Method get_edges()

Get edges data frame.

Usage

CographNetwork$get_edges()

Returns

Data frame with edge information.

Method get_layout()

Get layout coordinates.

Usage

CographNetwork$get_layout()

Returns

A data frame with x and y columns, or NULL when no layout is set.

Method get_node_aes()

Get node aesthetics.

Usage

CographNetwork$get_node_aes()

Returns

List of node aesthetic parameters.

Method get_edge_aes()

Get edge aesthetics.

Usage

CographNetwork$get_edge_aes()

Returns

List of edge aesthetic parameters.

Method get_theme()

Get theme.

Usage

CographNetwork$get_theme()

Returns

The stored theme (a CographTheme object or theme name), or NULL.

Method set_layout_info()

Set layout info.

Usage

CographNetwork$set_layout_info(info)

Arguments

info

List with layout information (name, seed, etc.).

Returns

The object itself, invisibly.

Method get_layout_info()

Get layout info.

Usage

CographNetwork$get_layout_info()

Returns

List with layout information.

Method set_plot_params()

Set plot parameters.

Usage

CographNetwork$set_plot_params(params)

Arguments

params

List of all plot parameters used.

Returns

The object itself, invisibly.

Method get_plot_params()

Get plot parameters.

Usage

CographNetwork$get_plot_params()

Returns

List of plot parameters.

Method print()

Print network summary.

Usage

CographNetwork$print()

Returns

The object itself, invisibly.

Method clone()

The objects of this class are cloneable with this method.

Usage

CographNetwork$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

CographNetwork$new(regulation_net)
#> CographNetwork
#>   Nodes: 10 
#>   Edges: 30 
#>   Directed: TRUE 
#>   Layout: none