Rgraphviz v2.16.0

Provides plotting capabilities for R graph objects

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

Readme

R package: Rgraphviz

This is the developer version of Bioconductor package Rgraphviz. Install in R as:

source('http://bioconductor.org/biocLite.R')
biocLite('Rgraphviz')

Additional installation tips

Rgraphviz now comes bundles with Graphviz. This should greatly simplify installation on all platforms, compared with earlier versions.

While it should not be necessary, we still allow for the use of an external Graphviz (external to Rgraphviz) at install time, except on Windows (this used to be supported on Windows but this is no longer true). This is indicated by the configure option --with-graphviz.

A direct specification of an external Graphviz at install time would be

R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz

In this case (with $DIR=/usr/local), the configure script assumes the presence of

$DIR/include/graphviz
$DIR/lib/graphviz

as is the default when Graphviz is installed. It is not possible to directly specifify these two directories, only $DIR

It is also possible to get Rgraphviz to search for Graphviz, by leaving the --with-graphviz option empty, as

R CMD INSTALL --configure-args='--with-graphviz' Rgraphviz_*.tar.gz

In this case, Rgraphviz will search for Graphviz using the following methods

  1. First try pkg-config
  2. See if Graphviz is in its default location of /usr/local

Notes

The release version of Graphviz 2.28 contains bugs that makes it not work with Rgraphviz for certain layout options. The patches to the bundled Graphviz 2.28.0 are included in package.

R CMD check results

Bioconductor: Multiple platform build/check report

Functions in Rgraphviz

Name Description
AgEdge-class Class "AgEdge": A class to describe an edge for a Ragraph object
removedEdges A Function To List Removed Edges
graphvizVersion A function to determine graphviz library version
AgNode-class Class "AgNode": A class to describe a node for a Ragraph object
buildNodeList A function to build lists of node and edge objects
renderGraph Render a laid out graph object
AgTextLabel-class Class "AgTextLabel": Represents a graphviz text label
agopen A function to obtain a libgraph object
GraphvizLayouts Graphviz Layout Methods
pNode-class Class "pNode": A class to plot nodes
layoutGraph A function to compute layouts of graph objects
BezierCurve-class Class "BezierCurve": A class to describe a Bezier curve
GraphvizAttributes Graph Attributes for Rgraphviz
graphData-methods Get and set attributes of an Ragraph object
boundingBox-class Class "boundingBox": A class to describe the bounding box of a Ragraph
getDefaultAttrs Functions to generate and check global attribute lists
clusterData-methods Get and set attributes for a cluster of an Ragraph object
xyPoint-class Class "xyPoint": A class to represent a X/Y coordinate.
graphLayout A function to layout graph locations
graphvizCapabilities List capabilities of Graphviz
plot-methods Plot a graph object - methods
toDot-methods A Generic For Converting Objects To Dot
makeNodeAttrs make a list of character vectors that can be used as a value for the nodeAttrs argument in agopen
agwrite Read / write Ragraph objects
agopenSimple A function to obtain a Ragraph object
Ragraph-class Class "Ragraph": A class to handle libgraph representations
pEdge-class Class "pEdge": A class to represent an edge
pieGlyph A function to plot pie graphs as a glyph
toFile Render a graph in a file with given format
graphDataDefaults-methods Get and set default attributes for an Ragraph
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Details

SystemRequirements optionally Graphviz (>= 2.16)
GraphvizDetails Graphviz 2.28.0
License EPL
LazyLoad Yes
Collate AllGenerics.R AllClasses.R SimpleMethods.R graphvizVersion.R graphviz_build_version.R agfunctions.R attrs.R graphLayout.R plotGraph.R plotUtils.R layoutGraph.R renderGraph.R graph_methods.R writers.R zzz.R
biocViews GraphAndNetwork, Visualization

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