sdnet (version 2.4.1)

cnPlot-method: Plot Network

Description

Draws the graph structure of catNetwork object or some diagnostic plots associated with a catNetworkEvaluate

Usage

cnPlot(object, file=NULL)

Arguments

object

catNetwork or catNetworkEvaluate object

file

a file name

Value

A R-plot or dot-file or pdf-file.

Details

First we consider the case when object is a catNetwork. There are two visualization options implemented - one using 'igraph' and the other 'Graphviz'. The usage of these two alternatives is controlled by two environment variables - the logical one R_CATNET_USE_IGRAPH and the character one R_DOTVIEWER, correspondingly. If igraph is installed and R_CATNET_USE_IGRAPH is set to TRUE, the function constructs an igraph compatible object corresponding to the object and plot it.

If igraph is not found, the function generates a dot-file with name file.dot, if file is specified, or unknown.dot otherwise. Furthermore, provided that Graphviz library is found and R_DOTVIEWER points to the dot-file executable, the created earlier dot-file will be compiled to pdf or postscript, if object is a list. Finally, if the system has pdf or postscript rendering capabilities and R_PDFVIEWER variable shows the path to the pdf-rendering application, the resulting pdf-file will be shown.

In case object is of class catNetworkEvaluate, then the function draws six relevant plots: likelihood vs. complexity, Hamming (hamm) and exponential Hamming (hammexp) distances, Markov neighbor distance (FP plus FN), and the false positive (fp) and false negative (fn) edges vs. complexity.

See Also

cnDot, catNetworkEvaluate-class, cnCompare

Examples

# NOT RUN {
  cnet <- cnRandomCatnet(numnodes=10, maxpars=3, numcats=2)
  cnPlot(object=cnet)
# }