Package 'hyperdraw'

Constructor for graphBPH objects

Description

A convenience constructor for graphBPH-class objects. This is a generic function.

Usage

graphBPH(graph, edgeNodePattern, ...)

Arguments

graph	Some form of graph that is to be converted into a graphBPH object.
edgeNodePattern	A regular expression used to distinguish between normal nodes and edge nodes.
...	Potential arguments to other methods.

Value

An object of class graphBPH-class

Methods

graphBPH

signature(graph = "graphNEL", edgeNodePattern = "character"): create a graphBPH object from a (directed) graphNEL object.

graphBPH

signature(graph = "Hypergraph", edgeNodePattern = "missing"): create a graphBPH object from a Hypergraph object (where all Hyperedges are DirectedHyperedges).

Author(s)

Paul Murrell

References

Falcon, S. and Gentleman, R. hypergraph: A package providing hypergraph data structures.

Gentleman, R. and Whalen, E. and Huber, W. and Falcon, S. graph: A package to handle graph data structures.

See Also

graphBPH-class

---

Class "graphBPH"

Description

A bipartite representation of a hypergraph. The purpose of this class is to support visualization of the hypergraph; it is not intended for analysis or manipulation of the hypergraph.

Objects from the Class

Objects can be created by calls of the form new("graphBPH", graph, edgeNodePattern, ...). There is also a convenience function graphBPH().

A graphBPH object consists of a graphNEL object, which must obey some strict rules:

• nodes in the graph are divided into two sets: normal nodes and edge-nodes,

• all edges in the graph must connect a normal node to an edge node,

• the graph must be a directed graph.

The edgeNodePattern is a regular expression that is used to define the set of edge-nodes.

Slots

graph:

Object of class graphNEL. This graph must obey the constraints described above.

edgeNodePattern:

Object of class character. The regular expression used to define edge-nodes.

nodes:

Object of class character. Records which nodes in the graph are normal nodes.

edgeNodes:

Object of class character. Records which nodes in the graph are edge-nodes.

edgeNodeIO:

Object of class list. Records information about which edges enter and exit each edge-node.

Methods

plot

signature(x = "graphBPH", y = "ANY"): draw a representation of the hypergraph where edges between normal nodes in the graph pass through an intermediate edge-node in a nice smooth curve.

graphLayout

signature(graph = "graphBPH", layoutType = "missing"): convert the graphBPH object to a RagraphBPH object (using a default layout method).

graphLayout

signature(graph = "graphBPH", layoutType = "character"): convert the graphBPH object to a RagraphBPH object (using the specified layout method).

Author(s)

Paul Murrell

References

Gansner, E.R. and and North, S.C. (1999) An open graph visualization system and its applications to software engineering, Software - Practice and Experience, 30:1203–1233.

Gentleman, R. and Whalen, E. and Huber, W. and Falcon, S. graph: A package to handle graph data structures.

Gentry, J. and Long, L. and Gentleman, R. and Falcon, S. and Hahne, F. and Sarkar, D. and Hansen, K. Rgraphviz: Provides plotting capabilities for R graph objects.

See Also

agopen, graphLayout and graphNEL RagraphBPH

Examples

nodes <- c(LETTERS[1:5], paste("R", 1:3, sep=""))
testgnel <- new("graphNEL",
                nodes=nodes,
                edgeL=list(
                  A=list(edges=c("R1", "R2")),
                  B=list(edges="R2"),
                  C=list(),
                  D=list(edges="R3"),
                  E=list(),
                  R1=list(edges="B"),
                  R2=list(edges=c("C", "D")),
                  R3=list(edges="E")),
                edgemode="directed")
testbph <- graphBPH(testgnel, "^R")
plot(testbph)

# A Hypergraph equivalent
require(hypergraph)
dh1 <- DirectedHyperedge("A", "B", "R1")
dh2 <- DirectedHyperedge(c("A", "B"), c("C", "D"), "R2")
dh3 <- DirectedHyperedge("D", "E", "R3")
hg <- Hypergraph(LETTERS[1:5], list(dh1, dh2, dh3))
plot(graphBPH(hg))

---

Layout a graph.

Description

This function is designed to layout a graph using the Rgraphviz package. The hyperdraw package makes this a generic function with a method for graphBPH objects. The function of the same name in the Rgraphviz package is used as a method for Ragraph objects.

Usage

graphLayout(graph, layoutType, ...)

Arguments

graph	An graphBPH object, which is to be laid out.
layoutType	The layout method (e.g., dot or neato).
...	These arguments will be passed to the agopen() function.

Value

An RagraphBPH object.

Author(s)

Paul Murrell

References

Gansner, E.R. and and North, S.C. (1999) An open graph visualization system and its applications to software engineering, Software - Practice and Experience, 30:1203–1233.

Gentry, J. and Long, L. and Gentleman, R. and Falcon, S. and Hahne, F. and Sarkar, D. and Hansen, K. Rgraphviz: Provides plotting capabilities for R graph objects.

See Also

agopen and GraphvizLayouts

Examples

nodes <- c(LETTERS[1:5], paste("R", 1:3, sep=""))
testgnel <- new("graphNEL",
                nodes=nodes,
                edgeL=list(
                  A=list(edges=c("R1", "R2")),
                  B=list(edges="R2"),
                  C=list(),
                  D=list(edges="R3"),
                  E=list(),
                  R1=list(edges="B"),
                  R2=list(edges=c("C", "D")),
                  R3=list(edges="E")),
                edgemode="directed")
testbph <- new("graphBPH", testgnel, "^R")
testrabph <- graphLayout(testbph)

---

Class "RagraphBPH"

Description

The purpose of this class is to represent a laid out version of a graphBPH object. The laying out is performed by the Rgraphviz package. This is an intermediate step in the process of drawing a graphBPH object.

Objects from the Class

Objects of this class should be created via the graphLayout() function.

Slots

graph:

Object of class Ragraph. The laid out graph.

allNodes:

Object of class character. The names of all nodes in the graph.

nodes:

Object of class character. Records normal nodes in the graph.

edgeNodes:

Object of class character. Records edge-nodes in the graph.

edgeNodeIO:

Object of class list. Records which edges enter and exit each edge-node.

Methods

plot

signature(x = "RagraphBPH", y = "ANY"): draw a representation of the hypergraph where edges between normal nodes in the graph pass through an intermediate edge-node in a nice smooth curve.

edgeDataDefaults<-

signature(self = "RagraphBPH", attr = "character", value = "ANY"): set the default drawing attributes for all edges.

edgeData<-

signature(self = "RagraphBPH", from = "character", to = "character", attr = "character", value = "ANY"): set a specific drawing attribute for one or more edges.

nodeDataDefaults<-

signature(self = "RagraphBPH", attr = "character", value = "ANY"): set the default drawing attributes for all nodes.

nodeData<-

signature(self = "RagraphBPH", n = "character", attr = "character", value = "ANY"): set a specific attribute for one or more nodes.

graphDataDefaults<-

signature(self = "RagraphBPH", attr = "character", value = "ANY"): set the default drawing attributes for the graph.

graphData<-

signature(self = "RagraphBPH", n = "character", attr = "character", value = "ANY"): set a specific attribute for the graph.

Author(s)

Paul Murrell

See Also

graphLayout, graphBPH, and Ragraph

Examples

nodes <- c(LETTERS[1:5], paste("R", 1:3, sep=""))
testgnel <- new("graphNEL",
                nodes=nodes,
                edgeL=list(
                  A=list(edges=c("R1", "R2")),
                  B=list(edges="R2"),
                  C=list(),
                  D=list(edges="R3"),
                  E=list(),
                  R1=list(edges="B"),
                  R2=list(edges=c("C", "D")),
                  R3=list(edges="E")),
                edgemode="directed")
testbph <- graphBPH(testgnel, "^R")
testrabph <- graphLayout(testbph)
edgeDataDefaults(testrabph, "lwd") <- 1
edgeData(testrabph, c("A", "R1"), c("R1", "B"), "lwd") <- c("3", 5)
edgeDataDefaults(testrabph, "color") <- "black"
edgeData(testrabph, c("A", "R1"), c("R1", "B"), "color") <- "red"
nodeDataDefaults(testrabph, "margin") <- 'unit(2, "mm")'
nodeDataDefaults(testrabph, "shape") <- "circle"
plot(testrabph)
graphDataDefaults(testrabph, "arrowLoc") <- "middle"
graphData(testrabph, "arrowLoc") <- "end"
plot(testrabph)
graphData(testrabph, "arrowLoc") <- "none"
plot(testrabph)

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