trigger-netPlot2ps: Write the network from a trigger probability matrix to a...

In igbucur/trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description

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

Usage

  ## 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)

Arguments

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.

Details

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.

Author(s)

Lin S. Chen [e-mail], Dipen P. Sangurdekar [e-mail] and John D. Storey [e-mail]

See Also

trigger.link and trigger.mlink

Examples

## 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)

igbucur/trigger documentation built on Oct. 16, 2020, 1:57 a.m.