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 
graph 
An object of class 
name 
The name of the 
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

graph
is from the package graphclass
.
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:
Determine the direction of the graph from the graph
object. This is the default and the recommended method.
An undirected graph
A directed graph
A strict undirected graph
A strict directed graph
Strict graphs do not allow self arcs or multiedges.
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@isbsib.ch>
http://www.research.att.com/sw/tools/graphviz/
1 2 3 4 5 6 7 8 9  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
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