graphviz.plot {bnlearn} R Documentation

Advanced Bayesian network plots

Description

Plot the graph associated with a Bayesian network using the Rgraphviz package.

Usage

graphviz.plot(x, highlight = NULL, groups, layout = "dot",
  shape = "circle", fontsize = 12, main = NULL, sub = NULL,
  render = TRUE)

Arguments

x

an object of class bn or bn.fit.

highlight

a list, see below.

groups

a list of character vectors, representing groups of node labels of nodes that should be plotted close to each other.

layout

a character string, the layout argument that will be passed to Rgraphviz. Possible values are dots, neato, twopi, circo and fdp. See Rgraphviz documentation for details.

shape

a character string, the shape of the nodes. Can be circle, ellipse or rectangle.

fontsize

a positive number, the font size for the node labels.

main

a character string, the main title of the graph. It's plotted at the top of the graph.

sub

a character string, a subtitle which is plotted at the bottom of the graph.

render

a logical value. If TRUE, graphviz.plot() actually draws the figure in addition to returning the corresponding graph object. If FALSE, no figure is produced.

Details

The highlight argument is a list with at least one of the following elements:

  • nodes: a character vector, the labels of the nodes to be highlighted.

  • arcs: the arcs to be highlighted (a two-column matrix, whose columns are labeled from and to).

and optionally one or more of the following graphical parameters:

  • col: an integer or character string (the highlight colour for the arcs and the node frames). The default value is red.

  • textCol: an integer or character string (the highlight colour for the labels of the nodes). The default value is black.

  • fill: an integer or character string (the colour used as a background colour for the nodes). The default value is transparent.

  • lwd: a positive number (the line width of highlighted arcs). It overrides the line width settings in strength.plot(). The default value is to use the global settings of Rgraphviz.

  • lty: the line type of highlighted arcs. Possible values are 0, 1, 2, 3, 4, 5, 6, "blank", "solid", "dashed", "dotted", "dotdash", "longdash" and "twodash". The default value is to use the global settings of Rgraphviz.

Note that all these parameters take a single value that is then applied to all nodes and arcs that will be highlighted.

Value

graphviz.plot() returns invisibly the graph object produced from the network passed as the x argument. It can be further modified using the graph and Rgraphviz packages.

Author(s)

Marco Scutari

See Also

plot.bn.