plotSG: Plot the subgraph around a Specific Node in a Graph Object

In pcalg: Methods for Graphical Models and Causal Inference

Plot the subgraph around a Specific Node in a Graph Object

Description

Plots a subgraph for a specified starting node and a given graph. The subgraph consists of those nodes that can be reached from the starting node by passing no more than a specified number of edges.

Usage

plotSG(graphObj, y, dist, amat = NA, directed = TRUE,
       plot = requireNamespace("Rgraphviz"), main = ,
       cex.main = 1.25, font.main = par("font.main"), col.main=par("col.main"),
       ...)

Arguments

graphObj	An R object of class graph.
y	(integer) position of the starting node in the adjacency matrix.
dist	Distance of nodes included in subgraph from starting node y.
amat	Precomputed adjacency matrix of type amat.cpdag (optional)
directed	logical indicating if the subgraph should be directed.
plot	logical indicating if the subgraph should be plotted (or just returned). Defaults to true when Rgraphviz is installed.
main	title to be used, with a sensible default; see title.
cex.main, font.main, col.main	optional settings for the main title; see title.
...	optional arguments passed to the plot() from package Rgraphviz.

Details

Commencing at the starting point y the function looks for the neighbouring nodes. Beginning with direct parents and children it will continue hierarchically through the distances to y. Note that the neighbourhood does not depend on edge directions. If directed is true (as per default), the orientation of the edges is taken from the initial graph.

For the plotting, the package Rgraphviz must be installed.

Value

the desired subgraph is returned; invisibly, i.e., via invisible, if plot is true.

Author(s)

Daniel Stekhoven, then Martin Maechler.

Examples

## generate a random DAG:
p <- 10
set.seed(45)
myDAG <- randomDAG(p, prob = 0.3)

if(requireNamespace("Rgraphviz")) {
  ## plot whole the DAG
  plot(myDAG, main = "randomDAG(10, prob = 0.3)")

  op <- par(mfrow = c(3,2))
  ## plot the neighbours of node number 8 up to distance 1
  plotSG(myDAG, 8, 1, directed = TRUE)
  plotSG(myDAG, 8, 1, directed = FALSE)

  ## plot the neighbours of node number 8 up to distance 2
  plotSG(myDAG, 8, 2, directed = TRUE)
  plotSG(myDAG, 8, 2, directed = FALSE)

  ## plot the neighbours of node number 8 up to distance 3
  plotSG(myDAG, 8, 3, directed = TRUE)
  plotSG(myDAG, 8, 3, directed = FALSE)

  ## Note that the layout of the subgraph might be different than in the
  ## original graph, but the graph structure is identical
  par(op)
} else { ## without 'Rgraphviz'
  sg2d <- plotSG(myDAG, 8, 2, directed = TRUE,  plot=FALSE)
  sg2u <- plotSG(myDAG, 8, 2, directed = FALSE, plot=FALSE)
}

pcalg documentation built on May 29, 2024, 5:24 a.m.