plot.nem {nem}R Documentation

plot nested effect model

Description

plot graph of nested effect model, the marginal likelihood distribution or the posterior position of the effected genes

Usage

        plot.nem(x, what="graph", remove.singletons=FALSE, PDF=FALSE, filename="nemplot.pdf", thresh=0, transitiveReduction=FALSE, ...)

Arguments

x nem object to plot
what (i), "graph", (ii) "mLL" = likelihood distribution, (iii) "pos" = posterior position of effected genes
remove.singletons remove unconnected nodes from the graph plot
PDF output as PDF-file
filename filename of PDF-file
thresh if x has a real valued adjacency matrix (weight matrix), don't plot edges with weight <= thresh
transitiveReduction plot a transitively reduced graph
... other arguments to pass

Value

none

Author(s)

Florian Markowetz <URL: http://genomics.princeton.edu/~florian>

See Also

nem, score


[Package nem version 2.2.1 Index]