ggm.plot.graph {GeneNet} | R Documentation |
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.
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, ...)
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 |
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.
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.
Juliane Schaefer (http://www.stat.math.ethz.ch/~schaefer/) and Korbinian Strimmer (http://strimmerlab.org).
ggm.test.edges
, plot.graph
.
# 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" )