agopenSimple: A function to obtain a Ragraph 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 graphNEL 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.

1 2	agopenSimple(graph, name, kind = NULL, edgeMode=edgemode(graph), subGList=list(), recipEdges=c("combined", "distinct"))

`graph`	An object of class `graphNEL`
`name`	The name of the `Ragraph`
`kind`	The type of graph
`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`, TODO: use this

graph is from the package graph-class.

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.

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.

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.

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

Li Long <li.long@isb-sib.ch>

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 <- agopenSimple(g1,name="foo")
if(graphvizVersion() >= "2.10") {
  ## This example will only run with Graphviz >= 2.10
  plot(z, "twopi")
}

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
Warning message:
In if (graphvizVersion() >= "2.10") { :
  the condition has length > 1 and only the first element will be used