trigger.netPlot2ps-methods {trigger} | R Documentation |
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 |
trig.prob |
A network-Trigger regulatory probability matrix with putative regulator genes in rows and putative regulated genes in columns. See |
filenam |
The output file name, without extension. If the name is not specified, the network will be write to the files |
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 " |
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 |
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)