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Convert a tna object to cograph parameters

Source: R/from-qgraph.R
from_tna.Rd

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

Usage

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

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 NULL, which picks the number of digits from the matrix: 0 when every non-zero weight is a whole number (counts, as in ftna/ctna models) and 2 otherwise (probabilities). Edges whose weight rounds to zero at this precision are dropped unless show_zero_edges = TRUE.

show_zero_edges

Logical. A zero weight means that the edge is absent, so an edge whose weight rounds to zero at weight_digits is dropped. With TRUE each such edge is plotted at the smallest magnitude that weight_digits can express, with its original sign. Other weights are unchanged. Default: FALSE.

...

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

Value

Invisibly, a named list of plotting parameters (the weight matrix x, labels, directed, the donut settings and the visual defaults above, after the overrides in ...). It can be passed to splot() with do.call(). An input that is not a tna object raises an error.

Details

Conversion Process

The transition matrix (weights) supplies the edge weights, the state labels (labels) supply the node labels, and the initial state probabilities (inits) supply the donut_fill values. The donuts are plotted with donut_inner_ratio = 0.8.

Directedness is read from the tna object when it is recorded there. Otherwise a symmetric matrix is treated as undirected and an asymmetric matrix as directed.

TNA Visual Defaults

The following defaults are applied. Each can be overridden through ....

  • layout = "oval".

  • node_fill: the RColorBrewer Accent palette for up to 8 states, Set3 for 9 to 12 states, and a qualitative HCL palette for more.

  • node_size = 7.

  • edge_color = "#003355".

  • edge_labels = TRUE, with edge_label_size = 0.4 and edge_label_position = 0.7.

  • edge_label_style = "estimate" and edge_label_leading_zero = FALSE, so a label shows the weight alone without a leading zero (for example .42).

  • minimum = 0.01, so transitions weaker than 0.01 are not plotted.

  • For directed networks, arrow_size = 0.61, edge_start_style = "dotted" and edge_start_length = 0.2 (the first 20 percent of each edge is dotted).

See also

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

Examples

from_tna(tna::tna(regulation_net))