plot.nem: plot nested effect model

In nem: (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Description

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

Usage

	## 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",...)

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
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.

Value

none

Author(s)

Florian Markowetz, Holger Froehlich

See Also

nem, plotEffects, infer.edge.type

nem documentation built on Oct. 31, 2019, 2:12 a.m.