agopen: A function to obtain a libgraph object
In Rgraphviz: Provides plotting capabilities for R graph objects

Description Usage Arguments Details Value Author(s) References See Also Examples

This function will read in a graph object and create a Ragraph object, returning it for use in other functions. The graph represented by the Ragraph can be laidout in various formats.

agopen(graph, name, nodes, edges, kind = NULL, layout = TRUE,
       layoutType = "dot",
       attrs = list(), nodeAttrs = list(), edgeAttrs = list(),
       subGList = list(), edgeMode = edgemode(graph),
       recipEdges=c("combined", "distinct"))

`graph`	An object of class `graphNEL`
`nodes`	A list of `pNode` objects
`edges`	A list of `pEdge` objects
`name`	The name of the graph
`kind`	The type of graph
`layout`	Whether to layout the graph or not
`layoutType`	Defines the layout engine. Defaults to dot, and see `graphvizCapabilities()$layoutTypes` for possible values.
`attrs`	A list of graphviz attributes
`nodeAttrs`	A list of specific node attributes
`edgeAttrs`	A list of specific edge attributes
`subGList`	A list describing subgraphs for the graph parameter
`edgeMode`	Whether the graph is directed or undirected
`recipEdges`	How to handle reciprocated edges, defaults to `combined`

graph is from the package graph-class.

The user can specify either the graph parameter and/or a combination of nodes and edges. If either of the latter parameters are not specified then graph must be passed in, and is used in the functions buildNodeList and buildEdgeList (as appropriate - if nodes is passed in but edges is not, only buildEdgeList is called) which are default transformer functions to generate the pNode and pEdge lists for layout.

The edgeMode argument specifies whether the graph is to be laid out with directed or undirected edges. This parameter defaults to the edgemode of the graph argument - note that if graph was not passed in then edgeMode must be supplied.

The kind parameter works as follows:

NULL:: Determine the direction of the graph from the graph object. This is the default and the recommended method.
AGRAPH:: An undirected graph
AGDIGRAPH:: A directed graph
AGRAPHSTRICT:: A strict undirected graph
AGDIGRAPHSTRICT:: A strict directed graph

Strict graphs do not allow self arcs or multi-edges.

If layout is set to TRUE, then the libgraph routines are used to compute the layout locations for the graph. Otherwise the graph is returned without layout information.

The subGList parameter is a list describing any subgraphs, where each element represents a subgraph and is itself a list with up to three elements. The first element, graph is required and contains the actual graph object for the subgraph. The second element, cluster is a logical value indicating if this is a cluster or a subgraph (a value of TRUE indicates a cluster, which is also the default value if this element is not specified). In Graphviz, subgraphs are more of an organizational mechanism, whereas clusters are laid out separately from the main graph and then later inserted. The last element of the list, attrs is used if there are any attributes for this subgraph. This is a named vector where the names are the attributes and the elements are the values for those attributes.

For a description of attrs, nodeAttrs and edgeAttrs, see the Ragraph man page.

The recipEdges argument can be used to specify how to handle reciprocal edges. The default value, combined will combine any reciprocated edges into a single edge (and if the graph is directed, will by default place an arrowhead on both ends of the edge), while the other option is distinct which will draw to separate edges. Note that in the case of an undirected graph, every edge of a graphNEL is going to be reciprocal due to implementation issues.

An object of class Ragraph

Jeff Gentry

http://www.research.att.com/sw/tools/graphviz/

graphLayout, Ragraph, plot

set.seed(123)
V <- letters[1:10]
M <- 1:4
g1 <- randomGraph(V, M, .2)
z <- agopen(g1,name="foo")
z
z <- agopen(g1,name="foo",layoutType="neato")

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
[1] "A graph with 10 nodes."