ggm.plot.graph {GeneNet}R Documentation

Graphical Gaussian Models: Plotting the Network

Description

ggm.make.dot converts an edge list as obtained by ggm.test.edges into a "dot" file that can directly be used for plotting the network with graphviz.

ggm.make.graph converts an edge list as obtained by ggm.test.edges into a graph object.

show.edge.weights summarizes a graph object by prints a vector of weights for all edges contained in a graph. This function is convenient to gain a first impression of the graph (in particular if the "Rgraphviz" library is not installed).

ggm.plot.graph visualizes the network structure of the graphical Gaussian model using the Rgraphviz network plot package. The correlation coefficients can be printed as edge labels.

Usage

ggm.make.dot(filename, edge.list, node.labels, main=NULL, show.edge.labels=FALSE)
ggm.make.graph(edge.list, node.labels, drop.singles=FALSE)
show.edge.weights(gr)
ggm.plot.graph(gr, 
    layoutType=c("fdp", "neato", "circo", "dot", "twopi"), 
    show.edge.labels=FALSE, ...)

Arguments

filename name of file containg the "dot" commands for graphviz
edge.list a data frame, as obtained by ggm.test.edges, listing all edges to be included in the graph
node.labels a vector with labels for each node (will be converted to type character)
main title included in plot
show.edge.labels plot correlation values as edge labels (default: FALSE)
drop.singles remove unconnected nodes
gr a graph object
layoutType type of plot of the graph. Defaults to "fdp".
... options passed to plot functions

Details

For network plotting the software "graphviz" is employed (http://www.graphviz.org).

For the functions ggm.plot.graph and ggm.make.graph the "graph" and "Rgraphviz" infrastructure from the Bioconductor project (http://www.bioconductor.org) is required.

Value

ggm.make.dot produces a "dot" network description file that can directly be fed into graphviz in order to produce a plot of a network.
ggm.make.graph returns a graph object, suitable for plotting with functions from the "Rgraphviz" library.
show.edge.weights returns a vector of weights for all edges contained in a graph.
ggm.plot.graph plots the network on the current graphic device.

Author(s)

Juliane Schaefer (http://www.stat.math.ethz.ch/~schaefer/) and Korbinian Strimmer (http://strimmerlab.org).

See Also

ggm.test.edges, plot.graph.

Examples

# load GeneNet library
library("GeneNet")
 
# generate random network with 20 nodes and 10 percent edges (=19 edges)
true.pcor <- ggm.simulate.pcor(20, 0.1)

# convert to edge list 
test.results <- ggm.list.edges(true.pcor)[1:19,]

########  use graphviz directly to produce a plot ##########

# uncomment for actual use!

# nlab <- LETTERS[1:20]
# ggm.make.dot(filename="test.dot", test.results, nlab, main = "A graph") 
# system("fdp -T svg -o test.svg test.dot") # SVG format

########  use Rgraphviz produce a plot ##########

# uncomment for actual use!

# nlab <- LETTERS[1:20]
# gr <- ggm.make.graph( test.results, nlab) 
# gr 
# show.edge.weights(gr) 
# gr2 <- ggm.make.graph( test.results, nlab, drop.singles=TRUE) 
# gr2 

# plot network
# NOTE: this requires the installation of the "Rgraphviz" library
# ggm.plot.graph(gr, main = "A graph")
# ggm.plot.graph(gr2, main = "The same graph with singles removed" )

[Package GeneNet version 1.1.0 Index]