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Convert a qgraph object to cograph parameters

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

Extracts the network, the layout and the plotting arguments from a qgraph object and passes them to a cograph plotting engine. Node, edge and graph settings are read from the resolved graphAttributes of the object. The colors posCol, negCol and the theme are read from its Arguments.

Usage

from_qgraph(
  qgraph_object,
  engine = c("splot", "soplot"),
  plot = TRUE,
  weight_digits = 2,
  show_zero_edges = FALSE,
  preserve_node_size = FALSE,
  ...
)

Arguments

qgraph_object

Return value of qgraph::qgraph()

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 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.

preserve_node_size

Logical. If TRUE, use the node sizes extracted from the qgraph object. Default FALSE uses cograph's standard sizing.

...

Overrides for any extracted parameter, given by cograph name (for example threshold). The qgraph names minimum and cut are translated to threshold and edge_cutoff.

Value

Invisibly, a named list of plotting parameters (the weight matrix x, weight_digits, the layout and the extracted node, edge and graph settings, after the overrides in ...). It can be passed to splot() with do.call(). An input without an Arguments field that does not inherit from "qgraph" raises an error.

Details

Parameter Mapping

The following qgraph parameters are extracted and mapped to their cograph equivalents.

Node properties:

  • labels/names -> labels

  • color -> node_fill

  • width -> node_size (scaled by 1.3x) when preserve_node_size = TRUE

  • shape -> node_shape (mapped to cograph equivalents)

  • border.color -> node_border_color

  • border.width -> node_border_width

  • label.cex -> label_size

  • label.color -> label_color

Edge properties:

  • labels -> edge_labels

  • label.cex -> edge_label_size (scaled by 0.5x)

  • lty -> edge_style (numeric to name conversion)

  • curve -> curvature (only when qgraph resolved a single curvature for the whole graph)

  • asize -> arrow_size (scaled by 0.3x)

  • edge.label.position -> edge_label_position

Graph properties:

  • minimum -> threshold

  • maximum -> maximum

  • groups -> groups

  • directed -> directed

  • posCol/negCol -> edge_positive_color/edge_negative_color

  • theme -> theme

Pie and donut:

  • pie values -> donut_fill with donut_inner_ratio = 0.8 and donut_empty = FALSE

  • pieColor -> donut_color

Settings that are not extracted

The edge colors and widths are not extracted, because qgraph stores them with its cut-based fading applied. cograph styles the edges by weight instead. The cut value is not extracted either.

Layout

The qgraph layout coordinates are kept with rescale = FALSE. When layout is supplied in ..., rescale is removed and the new layout is rescaled.

See also

cograph for creating networks from scratch, splot and soplot for plotting engines, from_tna for tna object conversion

Examples

q <- qgraph::qgraph(regulation_net, DoNotPlot = TRUE)
from_qgraph(q)