ggm.plot.graph {GeneTS} | R Documentation |
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.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, ...)
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) |
drop.singles |
remove unconnected nodes |
gr |
a graph object |
layoutType |
type of plot of the graph. Defaults to "fdp". |
show.edge.labels |
plot correlation values as edge labels (default: FALSE) |
... |
options passed to plot functions |
The network plotting functions require the installation of the "graph" and "Rgraphviz" R packages. These are available from the Bioconductor website (http://www.bioconductor.org). Note that it is not necessary to install the complete set of Bioconductor packages, only "graph" and "Rgraphviz" are needed by the GeneTS package (however, these may in turn require additional packages from Bioconductor).
ggm.plot.graph
is a utility function to plot a graph in "dfp" layout format.
The line width and color depends on the relative strength of the partial correlation
assigned to an edge: the top 80
the range from 20
20
The "Rgraphviz" package offers many other options - please consult the manual of "Rgraphviz" for the details.
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://www.statistik.lmu.de/~strimmer/).
ggm.test.edges
, plot.graph
.
# load GeneTS library library("GeneTS") # 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,] # generate graph object # NOTE: this requires the installation of the "graph" package # (in the following "try" is used to avoid an error if the library is not installed) nlab <- LETTERS[1:20] try( gr <- ggm.make.graph( test.results, nlab) ) try( gr ) try( show.edge.weights(gr) ) try( gr2 <- ggm.make.graph( test.results, nlab, drop.singles=TRUE) ) try( gr2 ) # plot network # NOTE: this requires the installation of the "Rgraphviz" library try ( ggm.plot.graph(gr, main = "A graph")) try ( ggm.plot.graph(gr2, main = "The same graph with singles removed" ))