trigger-netPlot2ps: Write the network from a trigger probability matrix to a...
In trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description Usage Arguments Details Author(s) See Also Examples

Write the network from a trigger probability matrix to a postscript file.

  ## S4 method for signature 'trigger'
trigger.netPlot2ps(triggerobj, trig.prob, filenam = NULL, pcut = 0.95, 
	layout = c("radial", "energy-minimized", "circular","hierarchical"),
	 node.color = NULL, edge.color = NULL, node.shape = NULL, nreg = 20)

`triggerobj`	An object of class `trigger`.
`trig.prob`	A network-Trigger regulatory probability matrix with putative regulator genes in rows and putative regulated genes in columns. See `trigger.net` for details.
`filenam`	The output file name, without extension. If the name is not specified, the network will be write to the files `temp.ps` and `temp.dot` at the current directory.
`pcut`	Threshold value for regulatory probabilities. The probabilities above the threshold are called significant and the corresponding regulatory relationships are plotted.
`layout`	The layout of the output network. One can choose from "`radial`" (default), "`energy-minimized`", "`circular`" or "`hierarchical`" layouts. You can specify just the initial letter.
`node.color`	The color of the nodes (genes). The default color is green.
`edge.color`	The color of the edges. The default color is blue.
`node.shape`	The shape of nodes (genes) if the number of regulatory relationships is below 1000. If that number is above 1000, the shape of nodes will be `dot`.
`nreg`	The number of top regulators to be selected. These selected top regulators will be plotted in red ellipses with their gene names labeled inside.

To use this function, please install the software Graphviz, which is available at http://www.graphviz.org/. For large networks, layout "radial" or "energy-minimized" is recommended. If the total number of significant regulatory relationships (directed edges) of the network is below 1000, we plot each node (gene) as a "box" with its name labeled inside. Otherwise, we plot each gene as a "dot" without name labeled to facilitate visualization. The top nreg (by default nreg = 20) regulators will be plotted in red ellipses labeled with their names.

See manual of Graphviz for other available colors and shapes of nodes.

Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu

trigger.link and trigger.mlink

## Not run: 
 data(yeast)
  attach(yeast)
  triggerobj <- trigger.build(marker = marker, exp = exp, 
				marker.pos = marker.pos, exp.pos = exp.pos)
  triggerobj <- trigger.loclink(triggerobj, window.size = 30000)
  trig.prob <- trigger.net(triggerobj, Bsec = 100)

  trigger.netPlot2ps(trig.prob, pcut = 0.95, layout = "e", filenam = "net95", nreg = 20)
  
  detach(yeast)

## End(Not run)