Ragraph-class: Class "Ragraph": A class to handle libgraph representations
In Rgraphviz: Provides plotting capabilities for R graph objects

Description Objects from the Class Slots Methods Author(s) See Also Examples

Class Ragraph is used to handle libgraph representations of R graph objects.

Objects can be created by calls to the function agopen.

agraph:: Object of class "externalptr": A C based structure containing the libgraph information
laidout:: Object of class "logical": Whether or not this graph has been laid out or not.
layoutType:: Object of class "character": The layout method used for this object
edgemode:: Object of class "character": The edgemode for this graph - “directed” or “undirected”
AgNode:: Object of class "list": A list of AgNode objects.
AgEdge:: Object of class "list": A list of AgEdge objects.
boundBox:: Object of class "boundBox": Defines the bounding box of the plot.
bg:: Object of class "character": The background color.
fg:: Object of class "character": The foreground color.

show: signature(object = "Ragraph"): A brief summary of the contents
agraph: signature(object = "Ragraph"): Returns the external libgraph pointer
laidout: signature(object = "Ragraph"): Returns the laidout slot
boundBox: signature(object = "Ragraph"): Returns the bounding box.
AgEdge: signature(object = "Ragraph"): Returns the edge list.
AgNode: signature(object = "Ragraph"): Returns the node list.
edgemode: signature(object = "Ragraph"): Retrieves the edgemode of this object.
layoutType: signature(object = "Ragraph"): Retrieves the method used for the layout of this graph.
edgeNames: signature(object = "Ragraph"): Returns a vector of the names of the edges in this graph.
graphDataDefaults: signature(self= "Ragraph"): Gets default attributes of the given graph.
graphDataDefaults<-: signature(self= "Ragraph", attr="vector", value="vector"): Sets default attributes of the given graph.
graphData: signature(self= "Ragraph", attr="vector"): Gets attributes of the given graph.
graphData<-: signature(self= "Ragraph", attr="vector", value="vector"): Sets attributes of the given graph.
clusterData: signature(self= "Ragraph", cluster="numeric", attr="vector"): Gets attributes of a cluster for the given graph.
clusterData<-: signature(self= "Ragraph", cluster="numeric", attr="vector", value="vector"): Sets attributes of a cluster for the given graph.
edgeDataDefaults: signature(self= "Ragraph",attr="missing"): Gets default attributes of the given edge.
edgeDataDefaults<-: signature(self= "Ragraph", attr="vector", value="vector"): Sets default attributes of the given edge.
edgeData: signature(self= "Ragraph", from="vector", to="vector", attr="vector"): Gets attributes of the given edge.
edgeData<-: signature(self= "Ragraph", from="vector", to="vector", attr="vector", value="vector"): Sets attributes of the given edge.
nodeDataDefaults: signature(self= "Ragraph",attr="missing"): Gets default attributes of the given node.
nodeDataDefaults<-: signature(self= "Ragraph", attr="vector", value="vector"): Sets default attributes of the given node.
nodeData: signature(self= "Ragraph", n="vector", attr="vector"): Gets attributes of the given node.
nodeData<-: signature(self= "Ragraph", n="vector", attr="vector", value="vector"): Sets attributes of the given node.
getNodeXY: signature(object = "Ragraph"): Returns a two element list, the first element contains a numerical vector with the 'x' positions of every node in this graph, and the second element contains a numerical vector with the 'y' positions for every node in the graph.
getNodeHeight: signature(object = "Ragraph"): Returns a vector with the heights of every node in the graph
getNodeLW: signature(object = "Ragraph"): Returns a vector with the left width of every node in the graph.
getNodeRW: signature(object = "Ragraph"): Returns a vector with the right width of every node in the graph.

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

agopen

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

## The various methods in action

## These methods are all used to obtain positional information about nodes
getNodeXY(z)
getNodeHeight(z)
getNodeLW(z)
getNodeRW(z)

## Retrieve information about the edges in the graph
edgeNames(z)
edgemode(z)

## These get information about the layout
laidout(z)
layoutType(z)
boundBox(z)

## Used to retrieve the entire list of edges or nodes
AgEdge(z)
AgNode(z)

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."
$x
 [1] 147  62 377 147 147  62 259 195 370 482

$y
 [1] 477 387 117 297 207 117 477  27 477 477

 [1] 54 54 54 54 54 54 54 54 54 54
 [1] 27 27 27 27 27 27 27 27 27 27
 [1] 27 27 27 27 27 27 27 27 27 27
 [1] "a~b" "a~d" "a~e" "a~f" "a~h" "b~d" "b~e" "b~f" "b~h" "c~h" "d~e" "d~f"
[13] "d~h" "e~f" "e~h" "f~h"
[1] "undirected"
[1] TRUE
[1] "dot"
An object of class "boundingBox"
Slot "botLeft":
x: 0, y: 0

Slot "upRight":
x: 524, y: 504

[[1]]
An edge between b and a with 1 BezierCurve objects: 
129,456 114,442 95,421 81,407 

[[2]]
An edge between d and a with 1 BezierCurve objects: 
147,449 147,415 147,357 147,324 

[[3]]
An edge between e and a with 2 BezierCurve objects: 
158,452 174,413 201,334 183,270 
183,270 179,255 171,240 163,229 

[[4]]
An edge between f and a with 2 BezierCurve objects: 
121,470 92,463 47,447 26,414 
26,414 -27,325 25,194 50,141 

[[5]]
An edge between h and a with 3 BezierCurve objects: 
170,462 211,435 291,374 291,298 
291,298 291,298 291,298 291,206 
291,206 291,141 242,77 214,46 

[[6]]
An edge between d and b with 1 BezierCurve objects: 
81,366 95,352 115,331 129,317 

[[7]]
An edge between e and b with 2 BezierCurve objects: 
71,361 81,337 96,300 111,270 
111,270 118,256 126,241 133,230 

[[8]]
An edge between f and b with 1 BezierCurve objects: 
62,359 62,308 62,195 62,144 

[[9]]
An edge between h and b with 2 BezierCurve objects: 
50,362 23,309 -32,175 26,90 
26,90 58,43 129,31 168,28 

[[10]]
An edge between h and c with 1 BezierCurve objects: 
353,104 318,87 254,56 219,39 

[[11]]
An edge between e and d with 1 BezierCurve objects: 
147,269 147,258 147,245 147,234 

[[12]]
An edge between f and d with 2 BezierCurve objects: 
133,273 126,262 118,247 111,234 
111,234 96,203 81,166 71,142 

[[13]]
An edge between h and d with 2 BezierCurve objects: 
163,274 170,263 179,248 183,234 
183,234 202,171 200,93 197,54 

[[14]]
An edge between f and e with 1 BezierCurve objects: 
129,186 114,172 95,151 81,137 

[[15]]
An edge between h and e with 1 BezierCurve objects: 
154,180 163,146 179,86 188,53 

[[16]]
An edge between h and f with 1 BezierCurve objects: 
84,101 109,85 148,59 173,42 

[[1]]
An object of class "AgNode"
Slot "center":
x: 147, y: 477

Slot "name":
[1] "a"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "a"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 6

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[2]]
An object of class "AgNode"
Slot "center":
x: 62, y: 387

Slot "name":
[1] "b"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "b"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 7

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[3]]
An object of class "AgNode"
Slot "center":
x: 377, y: 117

Slot "name":
[1] "c"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "c"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 6

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[4]]
An object of class "AgNode"
Slot "center":
x: 147, y: 297

Slot "name":
[1] "d"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "d"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 7

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[5]]
An object of class "AgNode"
Slot "center":
x: 147, y: 207

Slot "name":
[1] "e"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "e"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 6

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[6]]
An object of class "AgNode"
Slot "center":
x: 62, y: 117

Slot "name":
[1] "f"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "f"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 4

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[7]]
An object of class "AgNode"
Slot "center":
x: 259, y: 477

Slot "name":
[1] "g"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "g"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 7

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[8]]
An object of class "AgNode"
Slot "center":
x: 195, y: 27

Slot "name":
[1] "h"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "h"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 7

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[9]]
An object of class "AgNode"
Slot "center":
x: 370, y: 477

Slot "name":
[1] "i"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "i"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 3

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""


[[10]]
An object of class "AgNode"
Slot "center":
x: 482, y: 477

Slot "name":
[1] "j"

Slot "txtLabel":
An object of class "AgTextLabel"
Slot "labelText":
[1] "j"

Slot "labelLoc":
x: 0, y: 0

Slot "labelJust":
[1] "n"

Slot "labelWidth":
[1] 3

Slot "labelColor":
[1] "black"

Slot "labelFontsize":
[1] 14


Slot "height":
[1] 54

Slot "rWidth":
[1] 27

Slot "lWidth":
[1] 27

Slot "color":
[1] "black"

Slot "fillcolor":
[1] "transparent"

Slot "shape":
[1] "circle"

Slot "style":
[1] ""