plot.nem: plot nested effect model
In cbg-ethz/pcNEM: Probabilistic combinatorial nested effects model

Description Usage Arguments Value Author(s) See Also

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

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	## S3 method for class 'nem'
plot(x, what="graph", remove.singletons=FALSE, PDF=FALSE, filename="nemplot.pdf", thresh=0, transitiveReduction=FALSE, plot.probs=FALSE, SCC=TRUE, D=NULL, draw.lines=FALSE, palette="BlueRed",...)

`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
`plot.probs`	plot edge weights/probabilities. If regulation directions have been inferred (see `infer.edge.type`), upregulated edges are drawn red and downregulated edges blue. Edges, were no clear direction could be inferred, are drawn in black.
`SCC`	plot the strongly connected components graph
`D`	Visualize the nested subset structure of the dataset via `plotEffects` along with the graph and show the linking of E-genes to S-genes in the dataset. Should only be used for small networks. Default: Just plot the graph
`draw.lines`	If the nested subset structure is shown, should additionally lines connecting S-genes and their associated E-genes be drawn? WARNING: For larger datasets than e.g. 5 S-genes this most probably does not work, because the nested subset structure picture then partially overlaps with the graph picture. Default: Do not draw these lines
`palette`	color palette to use: either 'BlueRed' (default) or 'Grey'
`...`	other arguments to be passed to the Rgraphviz plot function or to the graphics 'image' function.