cnPlot: Plot Network

Description Usage Arguments Details Value Author(s) See Also Examples


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


cnPlot(object, file=NULL)



catNetwork or catNetworkEvaluate object


a file name


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, if file is specified, or 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.


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


N. Balov

See Also

cnDot, catNetworkEvaluate-class, cnCompare


  cnet <- cnRandomCatnet(numnodes=10, maxpars=3, numcats=2)

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