trigger.netPlot2ps-methods {trigger} | R Documentation

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

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

### 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)

[Package trigger version 1.40.0 Index]