cograph (version 1.5.2)

from_tna: Convert a tna object to cograph parameters

Description

Extracts the transition matrix, labels, and initial state probabilities from a tna object and plots with cograph. Initial probabilities are mapped to donut fills.

Usage

from_tna(
  tna_object,
  engine = c("splot", "soplot"),
  plot = TRUE,
  weight_digits = 2,
  show_zero_edges = FALSE,
  ...
)

Value

Invisibly, a named list of cograph parameters that can be passed to splot() or soplot().

Arguments

tna_object

A tna object from tna::tna()

engine

Which cograph renderer to use: "splot" or "soplot". Default: "splot".

plot

Logical. If TRUE (default), immediately plot using the chosen engine.

weight_digits

Number of decimal places to round edge weights to. Default 2. Edges that round to zero are removed unless show_zero_edges = TRUE.

show_zero_edges

Logical. If TRUE, keep edges even if their weight rounds to zero. Default: FALSE.

...

Additional parameters passed to the plotting engine (e.g., layout, node_fill, donut_color).

Details

Conversion Process

The tna object's transition matrix becomes edge weights, labels become node labels, and initial state probabilities (inits) are mapped to donut_fill values to visualize starting state distributions.

TNA networks are always treated as directed because transition matrices represent directional state changes.

The default donut_inner_ratio of 0.8 creates thin rings that effectively visualize probability values without obscuring node labels.

Parameter Mapping

The following tna properties are automatically extracted:

• weights: Transition matrix -> edge weights

• labels: State labels -> node labels

• inits: Initial probabilities -> donut_fill (0-1 scale)

TNA Visual Defaults

The following visual defaults are applied for TNA plots (all can be overridden via ...):

• layout = "oval": Oval/elliptical node arrangement

• node_fill: Colors from TNA palette (Accent/Set3 based on state count)

• node_size = 7: Larger nodes for readability

• arrow_size = 0.61: Prominent directional arrows

• edge_color = "#003355": Dark blue edges

• edge_labels = TRUE: Show transition weights on edges

• edge_label_size = 0.6: Readable edge labels

• edge_label_position = 0.7: Labels positioned toward target

• edge_start_style = "dotted": Dotted line at edge source

• edge_start_length = 0.2: 20% of edge is dotted

See Also

cograph for creating networks from scratch, splot and soplot for plotting engines, from_qgraph for qgraph object conversion

Examples

# Convert and plot a tna object
if (requireNamespace("tna", quietly = TRUE)) {
  library(tna)
  trans <- tna(group_regulation)
  from_tna(trans)  # Plots with donut rings showing initial probabilities

  # Use soplot engine instead
  from_tna(trans, engine = "soplot")

  # Customize the visualization
  from_tna(trans, layout = "circle", donut_color = c("steelblue", "gray90"))

  # Extract parameters without plotting
  params <- from_tna(trans, plot = FALSE)
  # Modify and plot manually
  params$node_fill <- "coral"
  do.call(splot, params)
}