# 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.

# R package: Rgraphviz

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

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


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 No Results!