| Title: | Provides plotting capabilities for R graph objects |
|---|---|
| Description: | Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. |
| Authors: | Kasper Daniel Hansen [cre, aut], Jeff Gentry [aut], Li Long [aut], Robert Gentleman [aut], Seth Falcon [aut], Florian Hahne [aut], Deepayan Sarkar [aut] |
| Maintainer: | Kasper Daniel Hansen <[email protected]> |
| License: | EPL |
| Version: | 2.51.0 |
| Built: | 2024-11-14 05:47:03 UTC |
| Source: | https://github.com/bioc/Rgraphviz |
This class is used to represent edges for the
Ragraph class. One can retrieve various pieces of information
as well as draw them.
Objects can be created by calls of the form new("AgEdge", ...).
arrowhead:Object of class "character" The
style of arrowhead for this edge.
arrowsize:Object of class "character" A scale
factor for the length of the arrow heads & tails
arrowtail:Object of class "character" The
style of arrowtail for this edge.
color:Object of class "character" The edge
color.
dir:Object of class "character" The edge direction.
ep:Object of class "xyPoint" The end point of
the edge.
head:Object of class "character" The head node
for this edge.
lty:Object of class "character" The edge
line type.
lwd:Object of class "numeric" The edge
line width.
sp:Object of class "xyPoint" The starting
point of the edge.
splines:Object of class "list" A list of
BezierCurve objects
tail:Object of class "character" The tail node
for this edge.
txtLabel:Object of class "character" The edge
text label.
Returns the splines slot
Returns the sp slot
Returns the ep slot
Returns the number of splines
Convenience method to retrieve a specific spline
Displays a concise description of the object
Draws the edge
Gets the head slot
Gets the tail slot
Returns any label for this edge
Retrieves the arrowhead slot.
Retrieves the arrowtail slot.
Retrieves the arrowsize slot.
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,name="foo") x <- AgEdge(z) ## list of AgEdge objects vv <- x[[1]] vv ## Demonstrate the methods of this class splines(vv) sp(vv) ep(vv) numSplines(vv) getSpline(vv, 1) head(vv) tail(vv) txtLabel(vv) arrowhead(vv) arrowtail(vv) arrowsize(vv)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,name="foo") x <- AgEdge(z) ## list of AgEdge objects vv <- x[[1]] vv ## Demonstrate the methods of this class splines(vv) sp(vv) ep(vv) numSplines(vv) getSpline(vv, 1) head(vv) tail(vv) txtLabel(vv) arrowhead(vv) arrowtail(vv) arrowsize(vv)
This class is used to represent nodes for the
Ragraph class. One can retrieve various pieces of information
as well as draw them.
Objects can be created by calls of the form new("AgNode", ...).
center:Object of class "xyPoint": The center
point of the node
name:Object of class "character": The name of
the node, used to reference it
txtLabel:Object of class "AgTextLabel": Label
for this edge
height:Object of class "integer": Height of
the node in points
rWidth:Object of class "integer": The right
half of the node in points.
lWidth:Object of class "integer": The left
half of the node in points.
color:Object of class "character": The drawing
color of the node.
fillcolor:Object of class "character": The
color to fill in the node with.
shape:Object of class "character": The shape
of the node.
style:Object of class "character": The style
of the node.
signature(object = "AgNode"): Retrieves the
drawing color for the node.
signature(object = "AgNode"): Retrieves the
color to fill in the node image with.
signature(object = "AgNode"): Returns
the center point of the node.
signature(object = "AgNode"): Returns the
center as a two element list, with the first element containing
the 'x' value and the second element containing the 'y' value.
signature(object = "AgNode"): Returns
the height of the node.
signature(object = "AgNode"): Returns the
left width of the node.
signature(object = "AgNode"): Returns the
right width of the node.
signature(object = "AgNode"): Retrieves the name
of the node.
signature(object = "AgNode"): Returns the shape
of the node.
signature(object = "AgNode"): Returns the style
of the node.
signature(object = "AgNode"): Retrieves the
node label.
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,name="foo") x <- AgNode(z) ## list of AgNode objects vv <- x[[1]] ## The methods in use color(vv) fillcolor(vv) getNodeCenter(vv) getNodeXY(vv) getNodeHeight(vv) getNodeLW(vv) getNodeRW(vv) name(vv) shape(vv) style(vv) txtLabel(vv)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,name="foo") x <- AgNode(z) ## list of AgNode objects vv <- x[[1]] ## The methods in use color(vv) fillcolor(vv) getNodeCenter(vv) getNodeXY(vv) getNodeHeight(vv) getNodeLW(vv) getNodeRW(vv) name(vv) shape(vv) style(vv) txtLabel(vv)
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"))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 |
nodes |
A list of |
edges |
A list of |
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
|
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
|
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:
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 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/
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")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")
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.
agopenSimple(graph, name, kind = NULL, edgeMode=edgemode(graph), subGList=list(), recipEdges=c("combined", "distinct"))agopenSimple(graph, name, kind = NULL, edgeMode=edgemode(graph), subGList=list(), recipEdges=c("combined", "distinct"))
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 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:
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 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 <[email protected]>
http://www.research.att.com/sw/tools/graphviz/
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopenSimple(g1,name="foo") if(graphvizVersion()$installed_version >= "2.10") { ## This example will only run with Graphviz >= 2.10 plot(z, "twopi") }set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopenSimple(g1,name="foo") if(graphvizVersion()$installed_version >= "2.10") { ## This example will only run with Graphviz >= 2.10 plot(z, "twopi") }
This class is used to represent the textlabel object in C from the Graphviz library
Objects can be created by calls of the form new("AgTextLabel", ...).
labelText:Object of class "character" The
actual label text
labelLoc:Object of class "xyPoint" The
location of the label
labelJust:Object of class "character" The
justification of the label
labelWidth:Object of class "integer" The width
of the label
labelColor:Object of class "character" The
color to print the label
labelFontsize:Object of class "numeric" The
font size for the label
Retrieves the labelText slot
Retrieves the labelLoc slot
Retrieves the labelJust slot
Retrieves the labelWidth slot
Retrieves the labelColor slot
Retrieves the labelFontsize slot
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) ## Make the labels be the edge weights. This code is from the vignette eAttrs <- list() ew <- edgeWeights(g1) lw <- unlist(unlist(ew)) toRemove <- removedEdges(g1) lw <- lw[-toRemove] names(lw) <- edgeNames(g1) eAttrs$label <- lw z <- agopen(g1,"foo", edgeAttrs=eAttrs) x <- AgEdge(z) ## list of AgEdge objects x[[1]] ## AgEdge a <- txtLabel(x[[1]]) a ## txtLabel object labelText(a) labelLoc(a) labelJust(a) labelWidth(a) labelColor(a) labelFontsize(a)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) ## Make the labels be the edge weights. This code is from the vignette eAttrs <- list() ew <- edgeWeights(g1) lw <- unlist(unlist(ew)) toRemove <- removedEdges(g1) lw <- lw[-toRemove] names(lw) <- edgeNames(g1) eAttrs$label <- lw z <- agopen(g1,"foo", edgeAttrs=eAttrs) x <- AgEdge(z) ## list of AgEdge objects x[[1]] ## AgEdge a <- txtLabel(x[[1]]) a ## txtLabel object labelText(a) labelLoc(a) labelJust(a) labelWidth(a) labelColor(a) labelFontsize(a)
These functions will write an Ragraph object to or from a file.
agwrite(graph, filename) agread(filename, layoutType="dot", layout=TRUE)agwrite(graph, filename) agread(filename, layoutType="dot", layout=TRUE)
graph |
An object of class |
filename |
The input or output filename |
layoutType |
character(1) specifying the format of the input
file. must be one of |
layout |
logical(1) indicating whether |
These function are wrappers to agwrite() and agread() calls in Graphviz.
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1, "foo", layout=FALSE) ## default layoutType 'dot' file <- tempfile() agwrite(z, file) ## supported input types graphvizCapabilities()$layoutTypes g2 <- agread(file, layout=TRUE) if (interactive()) plot(g2)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1, "foo", layout=FALSE) ## default layoutType 'dot' file <- tempfile() agwrite(z, file) ## supported input types graphvizCapabilities()$layoutTypes g2 <- agread(file, layout=TRUE) if (interactive()) plot(g2)
This class is used to represent a Bezier curve in R, which can then be used for other applications, plotted, etc
Objects can be created by calls of the form new("BezierCurve", ...).
cPoints:Object of class "list": A list of
xyPoint objects, representing control points for the curve
cPoints:Returns the cPoints slot
pointList:Returns a list of all points having been
processed with teh getPoints method of xyPoint
bezierPoints:Returns a matrix giving x & y points (by column) for the complete Bezier curve
lines:Draws the Bezier curve
show:Provides a concise display of information
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo") x <- AgEdge(z) ## list of AgEdge objects x[[1]] ## AgEdge a <- splines(x[[1]])[[1]] a ## BezierCurve cPoints(a) pointList(a) bezierPoints(a)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo") x <- AgEdge(z) ## list of AgEdge objects x[[1]] ## AgEdge a <- splines(x[[1]])[[1]] a ## BezierCurve cPoints(a) pointList(a) bezierPoints(a)
The boundingBox class is used to describe the
dimensons of the bounding box for a laid out Ragraph
Objects can be created by calls of the form new("boundingBox", ...).
botLeft:Object of class "xyPoint" Defines the
bottom left point of the bounding box
upRight:Object of class "xyPoint" Defines the
upper right point of the bounding box
Retrieve the botLeft slot
Retrieve the upRight slot
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo") x <- boundBox(z) x botLeft(x) upRight(x)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo") x <- boundBox(z) x botLeft(x) upRight(x)
These functions can be used to generate lists of pNode and
pEdge objects from an object of class graph. These
lists can then be sent to Graphviz to initialize and layout the graph
for plotting.
buildNodeList(graph, nodeAttrs = list(), subGList=list(), defAttrs=list()) buildEdgeList(graph, recipEdges=c("combined", "distinct"), edgeAttrs = list(), subGList=list(), defAttrs=list())buildNodeList(graph, nodeAttrs = list(), subGList=list(), defAttrs=list()) buildEdgeList(graph, recipEdges=c("combined", "distinct"), edgeAttrs = list(), subGList=list(), defAttrs=list())
graph |
An object of class |
nodeAttrs |
A list of attributes for specific nodes |
edgeAttrs |
A list of attributes for specific edges |
subGList |
A list of any subgraphs to be used in Graphviz |
recipEdges |
How to deal with reciprocated edges |
defAttrs |
A list of attributes used to specify defaults. |
These functions will take either the nodes or the edges of the
specified graph and generate a list of either pNode or
pEdge objects.
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.
The nodeAttrs and edgeAttrs attribute lists are to be
used for cases where one wants to set an attribute on a node or an
edge that is not the default. In both cases, these are lists with the
names of the elements corresponding to a particular attribute and the
elements containing a named vector - the names of the vector are names
of either node or edge objects and the values in the vector are the
values for this attribute.
Note that with the edgeAttrs list, the name of the edges are in
a particular format where an edge between x and y is named x~y.
Note that even in an undirected graph that x~y is not the same
as y~x - the name must be in the same order that the edge was
defined as having.
The subGraph argument can be used to specify a list of
subgraphs that one wants to use for this plot. The buildXXXList
functions will determine if a particular node or edge is in one of the
subgraphs and note that in the object.
The defAttrs list is a list used to specify any default values
that one wishes to use. The element names corresponde to the
attribute and the value is the default for that particular attribute.
If there is no default specified in defAttrs for an attribute
declared in nodeAttrs or edgeAttrs, then the latter must
have a value for every node or edge in the graph. Otherwise, if a
default is supplied, that value is used for any node or edge not
explicitly defined for a particular attribute.
A list of class pNode or pEdge objects.
Jeff Gentry
agopen, plot.graph,
pNode,pEdge
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildEdgeList(g1) x <- buildNodeList(g1)set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildEdgeList(g1) x <- buildNodeList(g1)
Attributes of a graph can be accessed using clusterData.
There's no default attributes for clusters.
The attributes must be defined using graphDataDefaults.
clusterData(self, cluster, attr) clusterData(self, cluster, attr) <- valueclusterData(self, cluster, attr) clusterData(self, cluster, attr) <- value
self |
A |
cluster |
cluster number |
attr |
A |
value |
A |
Li Long <[email protected]>
g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz", package="graph")) g11_gz <- gzfile(system.file("GXL/graphExample-11.gxl.gz", package="graph")) if(require(XML)) { g1 <- fromGXL(g1_gz) g11 <- fromGXL(g11_gz) g1_11 <- join(g1, g11) sgl <- vector(mode="list", length=2) sgl[[1]] <- list(graph=g1, cluster=TRUE) sgl[[2]] <- list(graph=g11, cluster=TRUE) ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl) clusterData(ng, 1, c("bgcolor")) <- c("blue") clusterData(ng, 2, c("bgcolor")) <- c("red") toFile(ng, layoutType="dot", filename="g1_11_dot.ps", fileType="ps") }g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz", package="graph")) g11_gz <- gzfile(system.file("GXL/graphExample-11.gxl.gz", package="graph")) if(require(XML)) { g1 <- fromGXL(g1_gz) g11 <- fromGXL(g11_gz) g1_11 <- join(g1, g11) sgl <- vector(mode="list", length=2) sgl[[1]] <- list(graph=g1, cluster=TRUE) sgl[[2]] <- list(graph=g11, cluster=TRUE) ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl) clusterData(ng, 1, c("bgcolor")) <- c("blue") clusterData(ng, 2, c("bgcolor")) <- c("red") toFile(ng, layoutType="dot", filename="g1_11_dot.ps", fileType="ps") }
The getDefaultAttrs function can be used to generate a default
global attribute list for Graphviz. The checkAttrs function
can be used to verify that such a list is valid for use.
getDefaultAttrs(curAttrs = list(), layoutType = "dot") checkAttrs(attrs)getDefaultAttrs(curAttrs = list(), layoutType = "dot") checkAttrs(attrs)
curAttrs |
Any attributes currently defined |
layoutType |
The layout method being used. Defaults to dot, and
see |
attrs |
An attribute list of graphviz attributes |
The getDefaultAttrs function generates a four element list
(elements being “graph”, “cluster”, “node” and
“edge”). Contained in each is another list where the element
names correspond to attributes and the value is the value for that
attribute. This list can be used to set global attributes in
Graphviz, and the exact list returned by getDefaultAttrs
represents the values that are used as basic defaults.
The checkAttrs function can be used to verify that a global
attribute list is properly formed.
Jeff Gentry
z <- getDefaultAttrs() checkAttrs(z)z <- getDefaultAttrs() checkAttrs(z)
Attributes of a graph can be accessed using graphData.
The attributes could be defined using graphDataDefaults.
graphData(self, attr) graphData(self, attr) <- valuegraphData(self, attr) graphData(self, attr) <- value
self |
A |
attr |
A |
value |
A |
Li Long <[email protected]>
Get/Set default values for attributes associated with a graph.
graphDataDefaults(self) graphDataDefaults(self, attr) <- valuegraphDataDefaults(self) graphDataDefaults(self, attr) <- value
self |
A |
attr |
A |
value |
A |
Li Long <[email protected]>
This function will take an object of class Ragraph and will
perform a libgraph layout on the graph locations.
graphLayout(graph, layoutType=graph@layoutType)graphLayout(graph, layoutType=graph@layoutType)
graph |
An object of type |
layoutType |
layout algorithm to use |
If the graph has already been laid out, this function merely returns its parameter. Otherwise, it will perform a libgraph layout and retrieve the appropriate location information.
A laid out object of type Ragraph.
Jeff Gentry
V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo",layout=FALSE) x <- z a <- graphLayout(z)V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- agopen(g1,"foo",layout=FALSE) x <- z a <- graphLayout(z)
The following describes the allowable attributes to be used with Rgraphviz. Most of these are sent directly to Graphviz and will influence the plot layout, some of these are only cosmetic and stay in R. Users are referred to the Graphviz web documentation which contains some more detailed information on these attributes (and is our source).
General Graph Attributes:
bgcolor:Color for the entire canvas. The default is
to use transparent
center:Drawing is centered in the output canvas.
This is a boolean value with a default of FALSE.
fontcolor:Color used for text, defaulting to
black.
fontname:Font used for text. Default is Times Roman.
fontpath:Directory used to search for fonts
fontsize:Font size, in points, for text. This
attribute accepts doubles for values with a default of 14.0
and a minimum value of 1.0
label:Label for the graph. This is a string with
some extra escape sequences which can be used. The substring
\N is replaced by the name of the node, and the substring
\G by the name of the graph. For graph or cluster
attributes, \G is replaced by the name of the graph or
cluster. For edge attributes, the substring \N is
replaced by the name of the edge, and the substrings \T
and \H by the names of the tail and head nodes. The
default value for nodes is \N with everything else
defaulting to
labeljust:Subgraphs inherit cluster behavior for
labeljust. If r, the labels are right-justified within
the bounding rectangle. If l they are left-justified.
Otherwise the labels are centered. The default value is
c.
labelloc:Top/bottom placement for graph labels. A
value of t places the label at the top, b places
them at the bottom. By default root graph labels go on the bottom
and cluster labels go on the top.
layers:Specifies a linearly ordered list of layer
names attached to the graph. Only those components belonging to
the current layer appear. This attribute accepts a
layerList, which is list of strings separated by the
characters defined with the layersep attribute which
defines layer names and implicitly numbered 1,2,etc. The default
is which only uses one layer.
layersep:Separator characters used to split the layers into a list of names. The default is colons, tabs or spaces.
margin:Set X&Y margins of canvas in inches.
Specified using the notation val,val where each val is a
double.
orientation:If "[1L*]*", set graph orientation to
landscape. Used only if rotate is not defined. Default is
the empty string.
page:Width & height of output pages, in inches. If set
and smaller then the size of the layout, a rectangular
array of pages of the specified page size is overlaid on the
layout, with origins aligned in the lower-left corner, thereby
partitioning the layout into pages. The pages are then produced
one at a time in 'pagedir' order. Specified using the notion
val,val where each val is a double.
pagedir:If the page attribute is set and
applicable, this attribute specifies the order in which the pages
are emitted. This is limited to one of the 8 row or column major
orders. One of BL, BR, TR, RB,
RT, LB, or LT specifying the 8 row or column
major orders for traversing a rectangular array (the first
character corresponding to the major order and the second to the
minor order). The default value is BL
quantum:If 'quantum' > 0.0, node label dimensions
will be rounded to integral multiples of the quantum. This
attribute is of type double, with a default and minimum value of
0.0
ranksep:In dot, this gives the desired rank
separation in inches. If the value contains equally, the
centers of all the ranks are spaced equally apart. In twopi,
specifies the separation of concentric circles. This value is of
type double, with a minimum value of 0.02. In dot, the
default value is 0.5 and for twopi it is 1.0.
ratio:Sets the aspect ratio for the drawing. If numeric, defines aspect ratio. If it is 'fill' and 'size' has been set, node positions are scaled such that the final drawing fills exactly the specified size. If 'compress' and the 'size' attribute is set and the graph can not be drawn on a single page, then the drawing is compressed to fit in the given size. If 'auto', the 'page' attribute is set and the graph cannot be drawn on a single page, then 'size' is set to an “ideal” value. The default for this attribute is “fill”
rotate:If 90, set drawing orientation to landscape.
This attribute accepts integer values and defaults to 0
samplepoints:If the input graph defines the
'vertices' attribute, and output is dot or xdot, this gives the
number of points used to represent circles and ellipses. It plays
the same role in neato, when adjusting the layout to avoid
overlapping nodes. This attribute accepts integer values and
defaults to 8
size:Maximum width and height of drawing, in inches.
Specified using the notation val,val where each val is a
double. If not specified and there is a current output device,
the graph is scaled to fit into that device. If size is
not specified and there is no current output device, a plot region
of the default size will be opened and the graph scaled to match that.
start:Parameter used to determine the initial layout of nodes. By default, nodes are randomly placed in a square whose sides have length (number of nodes). The same seed is always used for the random number generator, so the initial placement is repeatable. If 'start' converts to an integer, this is used as a seed value for the RNG. If 'start' is "regular", the nodes are placed regularly about a circle. Finally if 'start' is defined, and not one of those cases, the current time is used to pick a seed. The default is the empty string.
Dot Only Attributes
clusterrank:Mode used for handling
clusters. If "local", a subgraph whose name begins with "cluster"
is given special treatment. The subgraph is laid out separately,
and then integrated as a unit into its parent graph. If the cluster has
a 'label' parameter, this label is displayed w/ the cluster.
Acceptable values are local, global or none -
with local being the default.
compound:Allow edges between clusters. This is a
boolean value with a default of FALSE
concentrate:Use edge concentrators. This is a
boolean value with a default of FALSE
mclimit:Scale factor used to alter the 'MinQuit' and
'MaxIter' parameters used during crossing minimization. This is a
double value with a default of 1.0
nodesep:Minimum space between two adjacent nodes of
the same rank, in inches. This is a double value with a default
of 0.25 and a minimum of 0.02
ordering:If out for a graph and n is a node in
G, then edges n->* appear left to right in the order that they
were defined.
rankdir:Determines if the layout is left-to-right or
top-to-bottom. Acceptable values are LR and TB with
the default being the latter.
remincross:If TRUE and there are multiple
clusters, run cross minimization a second time. Default is FALSE
searchsize:During network simplex, maximum number of edges
with negative cut values to search when looking for one with
minimum cut value. This is an integer value with a default of 30
showboxes:Debugging feature for postscript output, R only. Not currently implemented.
Neato Only Attributes
Damping:Factor damping force motions. On each
iteration, a node's movement is limited to this factor of its
potential motion. This is a double value with a default of
0.99 and a minimum value of 0.0
defaultdist:Default distance between nodes in
separate connected components. Only applicable if
pack=FALSE. Defaults to 1+(avg. len)*sqrt(|V|) and
has a minimum value of epsilon.
dim:Set the number of dimensions used for the
layout. This is an integer value with a default and minimum value
of 2.
epsilon:Terminating condition. If length squared of
all energy gradients are less than epsilon, the algorithm stops.
This is a double value with a default of .0001 times the
number of nodes.
maxiter:Sets the number of iterations used. This is
an integer value with the default of MAXINT.
model:If circuit, use circuit resistance model
to compute dissimilarity values, otherwise use shortest path.
Defaults to the empty string.
Twopi Only Attributes
root:Name of the node to use as the center of the layout. If not defined, will pick the most central node.
Not Dot Attributes
normalize:Normalize coordinates of final layout so
that the first point is at the origin, then rotate so that the
first edge is horizontal. This is a boolean value with a default
of FALSE.
overlap:If scale, remove node overlaps by
scaling. If FALSE, use Voronoi technique, otherwise leave
overlaps. Default is the empty string.
pack:If "true" or non-negative integer - each
connected component is laid out separately and then the graphs
are packed tightly. If pack has an integral value, this is used
as the size (in points) of a margin around each part; otherwise
a default margin of 8 is used. If 'false', the entire graph is
laid out together. For twopi layouts, this just sets the
margin. Default is FALSE
packmode:Indicates the granularity and method used
for packing. This will automatically turn on pack.
Acceptable values are node, clust and graph,
specifying the granularity of packing connected components when
pack=TRUE. The default is node.
sep:Fraction to increase polygons for purposes of
determining overlap. This is a double value with a default of 0.01.
splines:Draw edges as splines. This is a boolean
value with a default of TRUE.
voro_margin:Factor to scale up drawing to allow
margin for expansion in Voronoi technique. This is a double value
with a default of 0.05 and a minimum value of 0.0
Output Based
resolution:Number of pixels per inch on a display,
used for SVG output. The default for this attribute is
0.96 and it accepts values of type double.
stylesheet:A URL or pathname specifying a XML style sheet, for SVG output.
truecolor:Output relies on a truecolor color model,
used with bitmap outputs. This is a boolean value with a default
of FALSE
Misc
URL:Hyperlink incorporated into the output. For whole graphs, used as part of an image map. Not currently implemented
comment:A device dependent commentary. Not currently implemented.
nslimit:Number of iterations in network simplex applications. Used in computing node x coordinates
nslimit1:Same as nslimit but for ranking
nodes
outputorder:Specify order in which nodes and edges are drawn. R only
General Edge Attributes
arrowhead:Shape of the arrowhead. Currently somewhat
limited in what can be rendered in R as opposed to what is
available via Graphviz in that only open and none
are allowed. The open is used by default for directed
edges and none for undirected edges. R only(?)
arrowsize:Multiplicative scale factor for arrowheads,
type double. R only (?). This attribute accepts values of type
double with a default of 1.0 and minimum of 1.0.
arrowtail:Style of arrow on the tail node of an edge,
see arrowhead. For directed edges that with bidirectional
arrows, open is used. R only(?)
color:The color of the edge. Defaults to
black.
decorate:If TRUE, attach edge label to edge by a
2-segment polyline, underlining the label, then going to the
closest point of the spline. Default is FALSE. Currently
unimplemented.
dir:Edge type drawing, which ends should get the
arrowhead. R only(?). For directed graphs, this defaults to
forward and undirected graphs default to both.
Other possible values are both (arrows in both
directions) and back (Arrow on the tail only)
fontcolor:The color used for text. The
default value is black in R
fontname:Font used for text. Defaults to Times Roman. Currently unimplemented.
fontsize:Font size, used for text. Defaults to
14.0 with a minimum value of 1.0
headclip:Head of the edge is clipped to the boundary
of the head node, otherwise it goes to the center of the node.
This is a boolean value with the default of TRUE.
Currently unimplemented
headlabel:Label for the head of the edge. See
label in Graph Attributes for a description of
additional escape sequences. Currently unimplemented.
headport:Where on the node to aim the edges, uses
center,
n, s, e, nw, nw, se, and
sw. The default is center.
label:The edge label. See
label in Graph Attributes for a description of
additional escape sequences.
labelangle:Angle in degrees that the label is
rotated, as a double. Default is -25.0 with a minimum
value of -180.0. Currently unimplemented.
labeldistance:Multiplicative scaling factor adjusting
the distance that the label is from the node. This is a double
value with a default of 1.0 and a minimum value of 0.0.
layer:Specifies the layers that this edge is present,
type of layerRange. This is specified as a string in the
format layerID or layerIDslayerIDslayerID..., where
s is a character from the layersep attribute. The
layerID attribute can be all, a decimal integer or a
layer name. Defaults to the empty string.
style:Set line style for the edge. R only. Can be
one of dashed, dotted, solid, invis
and bold. Defaults to solid.
tailclip:Same as headclip except for the tail
of the edge. Defaults to TRUE. Currently unimplemented.
taillabel:Same as headlabel except for the
tail of the edge. Defaults to the empty string. Currently
unimplemented.
weight:The weight of the edge. This attribute is of
type double with a default of 0.75 and a minimum value of
0.01.
Dot Only Attributes
constraint:If FALSE, edge is not used in ranking
nodes. Default is TRUE.
lhead:Logical head of an edge. If compound is
TRUE, if lhead is defined and is the name of a cluster
containing the real head, then the edge is clipped to the boundary
of the cluster.
ltail:Same as lhead but for the tail of the
edge
minlen:Minimum edge length (rank difference between
head and tail). This is an integer value with a default of
1 and a minimum of 0.
samehead:Edges with the same head and samehead
value are aimed at the same point on the head node.
sametail:Same as samehead but for the tail of
the edge.
Neato Only Attributes
len:Preferred edge length, in inches. This attribute
accepts double values with a default of 1.0.
Misc
URL:Hyperlink incorporated into the output. Not currently supported
headURL:URL for the head of the edge. Not currently supported
headtooltip:If there's a headURL, annotation for a tooltip. R only, not currently supported
tailURL:Same as headURL but for the tail of an
edge
tailtooltip:Same as headtooltip but for the
head of an edge
tooltip:Same as headtooltip but for the edge
in general
showboxes:Debugging feature for postscript. Not currently supported
comment:Device dependent comment inserted into the output. Not currently supported
General Node Attributes
color:Basic drawing color for the node, corresponding
to the outside edge of the node. The interior of the node is
specified with the fillcolor attribute. Defaults to
black.
distortion:Distortion factor for
shape=polygon, positive values cause top to be larger then
bottom, negative is opposite. This is a double value with a
default of 0.0 and a minimum value of -100.0
fillcolor:Background color of the node. This
defaults to black.
fixedsize:Use only width and height
attributes, do not expand for the width of the label. This
defaults to TRUE.
fontcolor:Color used for text. This
defaults to black.
fontname:Font used for text. The default of this is Times Roman.
fontsize:Size of font for the text. This defaults to
14.0 with a minimum size of 1.0.
height:Height of the node, in inches. This attribute
accepts values as doubles with a default of 0.5 and a minimum
value of 0.02.
label:Label for the node. See label in
Graph Attributes for an explanation of extra escape sequences.
layer:Layers in which the node is present. See
layer in Edge Attributes for an explanation of
acceptable inputs.
peripheries:Set number of peripheries used in polygonal shapes and cluster boundaries. Note that user-defined shapes are treated as a form box shape, so the default peripheries value is 1 and the user-defined shape will be drawn in a bounding rectangle. Setting peripheries=0 will turn this off. Also, 1 is the maximum peripheries value for clusters. Not currently implemented.
pos:Position of the node (For neato layouts, this is
the initial position of the node). Specified using the notion
val,val where each val is a double.
regular:Force the polygon to be regular. Defaults to
FALSE.
shape:The shape of the node. Current acceptable
values are circle, rectangle, rect,
box and ellipse. The circle shape is the
default. Note that box, rect and rectangle
all correspond to the same actual shape.
sides:Number of sides if shape=polygon. This
is an integer value with a default value of 4 and a minimum
value of 0.
skew:Skew factor for shape=polygon. Positive
values skew the polygon to the right, negative to the left. This
is a double value with a default value of 0.0 and a minimum
value of -100.0.
style:Set style for the node boundary. R only. Can be
one of dashed, dotted, solid, invis
and bold. Defaults to solid.
width:Width of the node, in inches. Default is
0.75 with a minimum value of 0.01
Dot Only Attributes
group:If the end points of an edge belong to the same group, ie they have the same group attributes, parameters are set to avoid crossings and keep the edges straight
Neato Only Attributes
pin:If TRUE and node has a pos attribute on
input, neato prevents the node from moving from the input
position. The default for this attribute is FALSE.
Misc
tooltip:Annotated tooltip if URL exists. R only. Currently unsupported
toplabel:Label near the top of nodes of shape M*. Currently unsupported
URL:Hyperlink incorporated into the output. Not currently supported
bottomlabel:Same as toplabel but for the
bottom of the node
comment:Device dependent comment inserted into the output. Not currently supported
shapefill:If non-empty, if output is ps or svg and shape is 'espf', taken as a filename containing a device-dependent description of a node's shape. If non-empty for bitmap output (gif, jpg, etc), and shape set to 'custom', taken as the URL for a file containing the bitmap image for the node. For files on the local machine, the URL begins with "file://". For remote files, graphviz must have been configured to use a command such as curl to retrieve the files remotely. Currently unsupported
z:Provides z coordinates for the node in a 3D system. Currently unsupported
Different attributes are appropriate for different specific graph layout algorithms. Graphviz supports three different layout algorithms, dot, neato and twopi.
There is some tension between attributes that graphviz supports and those that we can support at the R level. Please let us know if there are situations that are not being handled appropriately.
All attributes are passed down to graphviz. However they can be later modified for rendering in R.
Jeff Gentry
http://www.graphviz.org/pub/scm/graphviz2/doc/info/attrs.html
plot.graph, agopen, GraphvizLayouts
List the capabilities of the installed Graphviz.
graphvizCapabilities()graphvizCapabilities()
A list of 5 character vectors. Each character vector describes the relevant capabilitis of Graphviz.
Kasper Daniel Hansen [email protected]
graphvizCapabilities()graphvizCapabilities()
The following describes the different layout methods that can be used
within Rgraphviz. Each layout method has its own particular
advantages and disadvantages and can have its own quirks. Currently
Rgraphviz supports three different layout methods: dot,
twopi and neato.
Portions of the layout descriptions were taken from documents provided
at http://www.research.att.com/sw/graphviz. The specific
documents are listed in the references section of this page.
The dot algorithm produces a ranked layout of a graph
honoring edge directions. It is particularly appropriate for displaying
hierarchies or directed acyclic graphs. The basic layout scheme is
attributed to Sugiyama et al. The specific algorithm used by
dot follows the steps described by Gansner et al.
dot draws a graph in four main phases. Knowing this helps you to
understand what kind of layouts dot makes and how you can control
them. The layout procedure used by dot relies on the graph being
acyclic. Thus, the first step is to break any cycles which occur in
the input graph by reversing the internal direction of certain
cyclic edges. The next step assigns nodes to discrete ranks or
levels. In a top-to-bottom drawing, ranks determine Y
coordinates. Edges that span more than one rank are broken into
chains of virtual nodes and unit-length edges. The third step
orders nodes within ranks to avoid crossings. The fourth step sets X
coordnates of nodes to keep edges short, and the final step routes
edge splines.
In dot, higher edge weights have the effect of causing edges
to be shorter and straighter.
Fine-tuning should be approached cautiously. dot works best when it can
makes a layout without much help or interference in its
placement of individual nodes and edges. Layouts can be adjusted
somewhat by increasing the weight of certain edges, and sometimes
even by rearranging the order of nodes and edges in the file. But
this can backfire because the layouts are not necessarily stable
with respect to changes in the input graph. One last adjustment can
invalidate all previous changes and make a very bad drawing.
neato is a program that makes layouts of undirected graphs
following the filter model of dot. Its layout heuristic
creates virtual physical models and runs an iterative solver to find
low energy configurations. An ideal spring is placed between every
pair of nodes such that its length is set to the shortest path distance
between the endpoints. The springs push the nodes so their geometric
distance in the layout approximates their path distance in the
graph.
In neato, the edge weight is the strength of the
corresponding spring.
As with dot, fine-tuning should be approached cautiously, as
often small changes can have a drastic effect and create a poor
looking layout.
The radial layout algorithm represented by twopi is conceptually the
simplest. It takes a node specified as the center of the
layout and the root of the generated spanning tree. The remaining
nodes are placed on a series of concentric circles about the center,
the circle used corresponding to the graph-theoretic distance from
the node to the center. Thus, for example, all of the neighbors of
the center node are placed on the first circle around the
center. The algorithm allocates angular slices to each branch of the
induced spanning tree to guarantee enough space for the tree on each
ring. It should be obvious from the description that the basic
version of the twopi algorithm relies on the graph being
connected.
Of great importance to the quality of the layout is the selection of
an appropriate center node. By default, the twopi will
randomly pick one of the nodes that are furthest from a leaf node,
where a leaf node is a node of degree 1. The root attribute
can be used to manually select a central node for the layout, and
users are encouraged to use this attribute to select a node which
provides a good quality layout. It often might not be obvious what
that node will be, as it will vary from graph to graph, so some
experimentation might be required.
As with dot and neato, fine-tuning should be approached
cautiously, as often small changes can have a drastic effect and create a poor
looking layout. The root node of the layout, as mentioned
before, can have a profound effect on the outcome of the layout and
care should be taken to select an appropriate one.
The circo layout method draws graphs using a circular layout
(see Six and Tollis, GD '99 and ALENEX '99, and Kaufmann and Wiese,
GD '02.) The tool identifies biconnected components and draws the
nodes of the component on a circle. The block-cutpoint tree is then
laid out using a recursive radial algorithm. Edge crossings within a
circle are minimized by placing as many edges on the circle's
perimeter as possible. In particular, if the component is
outerplanar, the component will have a planar layout.
If a node belongs to multiple non-trivial biconnected components, the layout puts the node in one of them. By default, this is the first non-trivial component found in the search from the root component.
The fdp layout draws undirected graphs using a spring model
similar to neato. It relies on a force-directed approach in
the spirit of Fruchterman and Reingold. The fdp model uses
springs only between nodes connected with an edge, and an electrical
repulsive force between all pairs of nodes. Also, it achieves a
layout by minimizing the forces rather than the energy of the system.
Jeff Gentry
http://www.research.att.com/sw/tools/graphviz/dotguide.pdf, http://www.research.att.com/sw/tools/graphviz/neatoguide.pdf, http://www.research.att.com/sw/tools/graphviz/libguide.pdf
GraphvizAttributes, plot.graph,
agopen
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) if (interactive()) { op <- par() on.exit(par=op) par(ask=TRUE) plot(g1, "dot") plot(g1, "neato") plot(g1, "twopi") }set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) if (interactive()) { op <- par() on.exit(par=op) par(ask=TRUE) plot(g1, "dot") plot(g1, "neato") plot(g1, "twopi") }
This function will query the graphviz libraries that the package was built against and report what version of Graphviz is being used.
graphvizVersion()graphvizVersion()
A list with three elements, two of class numeric_version. The first
element named installed_version represents the version of
Graphviz that is being used by the package. The second element named
build_version represents the version of Graphviz that was used
to build the package. A mismatch between these two versions may
indicate problems. The third element is a logical named
bundled_graphviz and indicates if Rgraphviz is using the
bundled Graphviz (default) or an external Graphviz.
Jeff Gentry, modified by Kasper Daniel Hansen
graphvizVersion()graphvizVersion()
This is a wrapper to layout graph objects using arbitrary layout engines. The default engine (and so far the only implemented engine) is ATT's Graphviz.
layoutGraph(x, layoutFun = layoutGraphviz, ...)layoutGraph(x, layoutFun = layoutGraphviz, ...)
x |
A graph object |
layoutFun |
A function that performs the graph layout and returns a graph object with all necessary rendering information |
... |
Further arguments that are passed to |
Layout of a graph and its rendering are two separate
processes. layoutGraph provides an API to use an arbitrary
algorithm for the layout. This is archived by abstraction of the
layout process into a separate function (layoutFun) with
well-defined inputs and outputs. The only requirements on the
layoutFun are to accept a graph object as input and to return a
valid graph object with all the necessary rendering information stored
in its renderInfo slot. This information comprises
for nodes:
the locations of the nodes, in the coordinate
system defined by bbox (see below).
the width components of the nodes,
lWidth+rWidth=total width.
the heights of the nodes.
node label locations.
the justification of the node labels.
node label text.
the node shape. Valid values are box,
rectangle, ellipse, plaintext, circle
and triangle.
for edges:
representation of the edge splines as a list of
BezierCurve objects.
edge label locations.
edge label text.
some of Graphviz's arrow shapes are
supported. Currently they are: open, normal,
dot, odot, box, obox, tee,
diamond, odiamond and none. In addition, a
user-defined function can be passed which needs to be able to deal
with 4 arguments: A list of xy coordinates for the center of the
arrowhead, and the graphical parameters col, lwd and
lty.
The edge direction. The special value both is
used when reciprocrated edges are to be collapsed.
To indicate that this information has been added to the graph, the
graph plotting function should also set the laidout flag in the
graphData slot to TRUE and add the bounding box
information (i.e., the coordinate system in which the graph is laid
out) in the format of a two-by-two matrix as item bbox in the
graphData slot.
AT&T's Graphviz is the default layout algorithm to use when
layoutGraph is called without a specific layoutFun
function. See agopen for details about how to tweak
Graphviz and the valid arguments that can be passed on through
.... The most common ones to set in this context might be
layoutType, which controls the type of layout to compute and
the nodeAttrs and edgeAttrs arguments, which control the
fine-tuning of nodes and edges.
An object inheriting from class graph
Please note that the layout needs to be recomputed whenever attributes
are changed which are bound to affect the position of nodes or
edges. This is for instance the case for the arrowhead and
arrowtail parameters.
Florian Hahne, Deepayan Sarkar
renderGraph,
graph.par,
nodeRenderInfo,
edgeRenderInfo,
agopen,
set.seed(123) V <- letters[1:5] M <- 1:2 g1 <- randomGraph(V, M, 0.5) edgemode(g1) <- "directed" x <- layoutGraph(g1) renderGraph(x) ## one of Graphviz's additional layout algorithms x <- layoutGraph(g1, layoutType="neato") renderGraph(x) ## some tweaks to Graphviz's node and edge attributes, ## including a user-defined arrowhead and node shape functions. myArrows <- function(x, ...) { for(i in 1:4) points(x,cex=i) } myNode <- function(x, col, fill, ...) symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1, runif(1)), inches=0.5, fg=col, bg=fill, add=TRUE) eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee")) nAtt <- list(shape=c(d="box", c="ellipse", a=myNode)) edgemode(g1) <- "directed" x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato") renderGraph(x)set.seed(123) V <- letters[1:5] M <- 1:2 g1 <- randomGraph(V, M, 0.5) edgemode(g1) <- "directed" x <- layoutGraph(g1) renderGraph(x) ## one of Graphviz's additional layout algorithms x <- layoutGraph(g1, layoutType="neato") renderGraph(x) ## some tweaks to Graphviz's node and edge attributes, ## including a user-defined arrowhead and node shape functions. myArrows <- function(x, ...) { for(i in 1:4) points(x,cex=i) } myNode <- function(x, col, fill, ...) symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1, runif(1)), inches=0.5, fg=col, bg=fill, add=TRUE) eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee")) nAtt <- list(shape=c(d="box", c="ellipse", a=myNode)) edgemode(g1) <- "directed" x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato") renderGraph(x)
make a list of character vectors that can be used as a value for the nodeAttrs argument in agopen
makeNodeAttrs(g, label = nodes(g), shape = "ellipse", fillcolor = "#e0e0e0", ...)makeNodeAttrs(g, label = nodes(g), shape = "ellipse", fillcolor = "#e0e0e0", ...)
g |
graph |
label |
character of length either |
shape |
character of length either |
fillcolor |
character of length either |
... |
further named arguments that are character vectors of length either 1 or numNodes(g) |
This function is trivial but convenient.
A list of named character vectors, each of which with
length numNodes(g).
Wolfgang Huber <[email protected]>
g <- randomEGraph(letters[1:10], p=0.2) makeNodeAttrs(g)g <- randomEGraph(letters[1:10], p=0.2) makeNodeAttrs(g)
This class is used to represent all necessary information to plot an edge in Graphviz
The attrs slot is a named list, where the names correspond to
attributes and the values in the list correspond to the value for that
element's attribute.
The subG slot describes which subgraph this edge is a part of.
A value of 0 implies that the edge is not a member of any subgraph.
Objects can be created by calls of the form new("pEdge", ...).
from:Object of class "character": The name of
the node on the tail of this edge.
to:Object of class "character": The name of
the node on the head of this edge.
attrs:Object of class "list": A list of
attributes specific to this edge.
subG:Object of class "integer": Which subgraph
this edge is a part of.
signature(object = "pEdge"): Retrieves the
from slot of this edge
signature(object = "pEdge"): Retrieves the
to slot of this edge
R. Gentleman and Jeff Gentry
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildEdgeList(g1) vv <- z[[1]] ## Object of type pEdge vv from(vv) to(vv)set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildEdgeList(g1) vv <- z[[1]] ## Object of type pEdge vv from(vv) to(vv)
This function allows the user to plot a pie graph at a specified x/y location in a plotting region.
pieGlyph(x, xpos, ypos, labels = names(x), edges = 200, radius = 0.8, density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL, ...)pieGlyph(x, xpos, ypos, labels = names(x), edges = 200, radius = 0.8, density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL, ...)
xpos |
The x location of the glyph |
ypos |
The Y location of the glyph |
x |
a vector of positive quantities.
The values in |
labels |
a vector of character strings giving names for the slices. For empty or NA labels, no pointing line is drawn either. |
edges |
the circular outline of the pie is approximated by a polygon with this many edges. |
radius |
the pie is drawn centered in a square box whose sides
range from |
density |
the density of shading lines, in lines per inch.
The default value of |
angle |
the slope of shading lines, given as an angle in degrees (counter-clockwise). |
col |
a vector of colors to be used in filling or shading
the slices. If missing a set of 6 pastel colours is used,
unless |
border, lty
|
(possibly vectors) arguments passed to
|
main |
an overall title for the plot. |
... |
graphical parameters can be given as arguments to
|
R. Gentleman, F. Sim
plot(1:10, col="white") pieGlyph(1:20, 5, 5)plot(1:10, col="white") pieGlyph(1:20, 5, 5)
A plot method for graph objects.
## S4 method for signature 'graph,ANY' plot(x, y, ..., name = "", subGList = list(), attrs = list(), nodeAttrs = list(), edgeAttrs = list(), recipEdges = c("combined", "distinct")) ## S4 method for signature 'Ragraph,ANY' plot(x, y, edgeAttrs = list(), ..., main = NULL, cex.main = NULL, col.main = "black", sub = NULL, cex.sub = NULL, col.sub = "black", drawNode = drawAgNode, xlab, ylab, mai)## S4 method for signature 'graph,ANY' plot(x, y, ..., name = "", subGList = list(), attrs = list(), nodeAttrs = list(), edgeAttrs = list(), recipEdges = c("combined", "distinct")) ## S4 method for signature 'Ragraph,ANY' plot(x, y, edgeAttrs = list(), ..., main = NULL, cex.main = NULL, col.main = "black", sub = NULL, cex.sub = NULL, col.sub = "black", drawNode = drawAgNode, xlab, ylab, mai)
x |
The |
y |
The layout method to use: One of |
name |
The name of the graph, passed to |
subGList |
A list of subgraphs taken from the primary
|
attrs |
A list of Graphviz attributes to be sent to the layout engine |
nodeAttrs |
A list of attributes for specific nodes |
edgeAttrs |
A list of attributes for specific edges |
recipEdges |
Determines how to draw reciprocating edges. See
|
main, cex.main, col.main
|
Main label and graphic parameters for the plot |
sub, cex.sub, col.sub
|
Subtitle and graphic parameters for the plot |
drawNode |
Function to draw the nodes. The default is
|
xlab |
Label for the x axis of the plot |
ylab |
Label for the y axis of the plot |
mai |
Margins for plot |
... |
General commands to be sent to plot |
The first plot method in the usage section corresponds to the
graph class in the graph package. It will convert the
graph object into an object of class Ragraph by using
Graphviz to perform the layout. Then it will call the plot method for
Ragraph. The plot.graph method is nothing more then a
wrapper that calls agopen and plot.Ragraph.
The second plot method in the usage section is for the
Ragraph class, which describes a Graphviz structure of a
graph. This method will extract necessary information from the object
and use it to plot the graph.
Users can specify arbitrary drawing functions for the nodes of the
Ragraph with the drawNode argument, although caution is
urged. The default drawing function for
all nodes is drawAgNode, which will draw a basic circle,
ellipse or rectangle according to the layout specifications for each
node. If supplying a custom function, users are encouraged to look at
the code of this function for a more clear picture of the information
required to properly draw a node. Users can specify either one
custom function to be used for all nodes or a list (where length is
equal to the nubmer of nodes) of functions where the Nth element in
the list provides the drawing function for the Nth node, and every
function will take four parameters - the first is an object of class
AgNode representing the node itself and the second is an object
of class xyPoint representing the upper right corner of
the Graphviz plotting region (where the lower left is 0,0).
The third parameter, attrs is a node attribute list and
represents post-layout attribute changes where the user wants to
override values present in the layout. The last argument,
radConv is a divisor to the radius and is used to convert from
Graphviz units to R plotting units. Outside of the first
argument, the rest of these (particularly radConv which
generally shouldn't be specifically set) do not need to be set by the
user, but any drawing function must have them as parameters.
The attrs list requires a particular format. It must be of
length 3 with names graph, node, and edge. Each
of these elements themselves are lists - such that an element of
graph corresponds to a graph element. A full listing of
attributes and their possible settings is available at
http://www.research.att.com/~erg/graphviz/info/attrs.html. All
attribute values should be entered as character strings (even if the
requested value is to be otherwise).
The nodeAttrs list is used to specify attributes on a
particular node, instead of for all nodes. The format of this list is
such that the elements correspond to attributes (the name of the
element is used to note which attribute) and each element contains a
named vector. The names of the vector denote which nodes are having
this attribute set and the values in the vector specify the value.
The edgeAttrs list is identical in format to nodeAttrs.
However, the name of the edges is in a particular format where an edge
between x and y is named x~y. Note that even in an undirected
graph that x~y is not the same as y~x - the name must be
in the same order that the edge was defined as having.
The Ragraph object used for plotting
Jeff Gentry
# WHY DOES THIS NOT WORK IN CHECK? # V <- letters[1:10] # M <- 1:4 # g1 <- randomGraph(V, M, .2) # plot(g1)# WHY DOES THIS NOT WORK IN CHECK? # V <- letters[1:10] # M <- 1:4 # g1 <- randomGraph(V, M, .2) # plot(g1)
This class is used to transfer information to Graphviz that is necessary to represent and plot a node.
The attrs slot is a named list, where the names correspond to
attributes and the values in the list correspond to the value for that
element's attribute.
The subG slot describes which subgraph this node is a part of.
A value of 0 implies that the node is not a member of any subgraph.
Objects can be created by calls of the form new("pNode", ...).
name:Object of class "character": The name of
the node, used to reference the node.
attrs:Object of class "list": A list of
attributes specific to this node.
subG:Object of class "integer": Which subgraph
this node is a part of.
signature(object = "pNode"): Retrieves the
name slot of the object.
R. Gentleman and Jeff Gentry
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildNodeList(g1) z[[1]] ## Object of type pNode name(z[[1]])set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) z <- buildNodeList(g1) z[[1]] ## Object of type pNode name(z[[1]])
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.
signature(object = "Ragraph"): A brief summary of
the contents
signature(object = "Ragraph"): Returns the
external libgraph pointer
signature(object = "Ragraph"): Returns the
laidout slot
signature(object = "Ragraph"): Returns the
bounding box.
signature(object = "Ragraph"): Returns the edge
list.
signature(object = "Ragraph"): Returns the node
list.
signature(object = "Ragraph"): Retrieves the
edgemode of this object.
signature(object = "Ragraph"): Retrieves the
method used for the layout of this graph.
signature(object = "Ragraph"): Returns a
vector of the names of the edges in this graph.
signature(self= "Ragraph"):
Gets default attributes of the given graph.
signature(self= "Ragraph", attr="vector", value="vector"):
Sets default attributes of the given graph.
signature(self= "Ragraph", attr="vector"):
Gets attributes of the given graph.
signature(self= "Ragraph", attr="vector", value="vector"):
Sets attributes of the given graph.
signature(self= "Ragraph", cluster="numeric", attr="vector"):
Gets attributes of a cluster for the given graph.
signature(self= "Ragraph", cluster="numeric", attr="vector", value="vector"):
Sets attributes of a cluster for the given graph.
signature(self= "Ragraph",attr="missing"):
Gets default attributes of the given edge.
signature(self= "Ragraph", attr="vector", value="vector"):
Sets default attributes of the given edge.
signature(self= "Ragraph", from="vector", to="vector", attr="vector"):
Gets attributes of the given edge.
signature(self= "Ragraph", from="vector", to="vector", attr="vector", value="vector"):
Sets attributes of the given edge.
signature(self= "Ragraph",attr="missing"):
Gets default attributes of the given node.
signature(self= "Ragraph", attr="vector", value="vector"):
Sets default attributes of the given node.
signature(self= "Ragraph", n="vector", attr="vector"):
Gets attributes of the given node.
signature(self= "Ragraph", n="vector", attr="vector", value="vector"):
Sets attributes of the given node.
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.
signature(object = "Ragraph"): Returns a
vector with the heights of every node in the graph
signature(object = "Ragraph"): Returns a
vector with the left width of every node in the graph.
signature(object = "Ragraph"): Returns a
vector with the right width of every node in the graph.
Jeff Gentry and Li Long <[email protected]>
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)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)
This function can be used to retrieve a numerical vector which will
describe which edges in a graph would be removed if recipEdges
is set to combined during plotting.
removedEdges(graph)removedEdges(graph)
graph |
An object of class |
This function will simply detect which (if any) edges in a graph would be removed during combination of reciprocated edges.
A numerical vector, where the values correspond to removed edges.
Jeff Gentry
edgeNames,
agopen, buildEdgeList
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) removedEdges(g1)set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) removedEdges(g1)
This method uses the renderInfo slot of a graph object to
render it on a plotting device. The graph must have been laid out
using the layoutGraph function before.
## S4 method for signature 'graph' renderGraph(x, ..., drawNodes="renderNodes", drawEdges=renderEdges, graph.pars=list())## S4 method for signature 'graph' renderGraph(x, ..., drawNodes="renderNodes", drawEdges=renderEdges, graph.pars=list())
x |
An object derived from class |
drawNodes |
A function that is used for the node rendering. The
details of its API are still undecided, so far the input to the
function is the (laid out) graph object. Defaults to
|
drawEdges |
A function that is used for the edge
rendering. Defaults to |
graph.pars |
A list of rendering parameters to use as
defaults. Parameters that have been explicitely set using
|
... |
further arguments |
This method can render graph objects that have previously been laid
out using the function layoutGraph. The details for user
defined node drawing remain to be decided.
An object derived from class graph with information about the
coordinates of the nodes in the coordinate system of the plotting
device added to the renderInfo slot.
Florian Hahne
layoutGraph,
link[graph:renderInfo-class]{nodeRenderInfo},
link[graph:renderInfo-class]{edgeRenderInfo},
link[graph:renderInfo-class]{graphRenderInfo},
set.seed(123) V <- letters[1:5] M <- 1:2 g1 <- randomGraph(V, M, 0.5) edgemode(g1) <- "directed" x <- layoutGraph(g1) renderGraph(x) ## one of Graphviz's additional layout algorithms x <- layoutGraph(g1, layoutType="neato") renderGraph(x) ## some tweaks to Graphviz's node and edge attributes, ## including a user-defined arrowhead and node shape functions. myArrows <- function(x, ...) { for(i in 1:4) points(x,cex=i) } myNode <- function(x, col, fill, ...) symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1, runif(1)), inches=0.5, fg=col, bg=fill, add=TRUE) eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee")) nAtt <- list(shape=c(d="box", c="ellipse", a=myNode)) edgemode(g1) <- "directed" x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato") renderGraph(x)set.seed(123) V <- letters[1:5] M <- 1:2 g1 <- randomGraph(V, M, 0.5) edgemode(g1) <- "directed" x <- layoutGraph(g1) renderGraph(x) ## one of Graphviz's additional layout algorithms x <- layoutGraph(g1, layoutType="neato") renderGraph(x) ## some tweaks to Graphviz's node and edge attributes, ## including a user-defined arrowhead and node shape functions. myArrows <- function(x, ...) { for(i in 1:4) points(x,cex=i) } myNode <- function(x, col, fill, ...) symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1, runif(1)), inches=0.5, fg=col, bg=fill, add=TRUE) eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee")) nAtt <- list(shape=c(d="box", c="ellipse", a=myNode)) edgemode(g1) <- "directed" x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato") renderGraph(x)
This generic is used to convert objects of varying classes to the Dot
language. Currently, only the graph class is supported.
toDot(graph, filename, ...)toDot(graph, filename, ...)
graph |
The |
filename |
The name of the file to output to. |
... |
Any arguments to pass on to |
The method defined for graph objects is a convenience wrapper
around agopen and agwrite in that order.
It will take an object of class graph (or one of its
subclasses), call agopen (any extra arguments besides the graph
and the name parameter should be passed in via ...)
and then write the resulting information via agwrite in
the file specified by filename.
Jeff Gentry
set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) nAttrs <- list() eAttrs <- list() nAttrs$label <- c(a="lab1", b="lab2", g="lab3", d="lab4") eAttrs$label <- c("a~h"="test", "c~h"="test2") nAttrs$color <- c(a="red", b="red", g="green", d="blue") eAttrs$color <- c("a~d"="blue", "c~h"="purple") toDot(g1, tempfile(), nodeAttrs=nAttrs, edgeAttrs=eAttrs)set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, .2) nAttrs <- list() eAttrs <- list() nAttrs$label <- c(a="lab1", b="lab2", g="lab3", d="lab4") eAttrs$label <- c("a~h"="test", "c~h"="test2") nAttrs$color <- c(a="red", b="red", g="green", d="blue") eAttrs$color <- c("a~d"="blue", "c~h"="purple") toDot(g1, tempfile(), nodeAttrs=nAttrs, edgeAttrs=eAttrs)
Render a graph in a file with given format
toFile(graph, layoutType = "dot", filename, fileType = "dot")toFile(graph, layoutType = "dot", filename, fileType = "dot")
graph |
an instance of the |
layoutType |
Which layout algorithm to use. Defaults to dot, and
see |
filename |
output file name |
fileType |
Output file type. Defaults to |
This function takes a given Ragraph, does the chosen layout, then
renders the output to an external file. Users could view the output file
with corresponding viewer.
toFile returns NULL after writing to a file.
Li Long <[email protected]>
Rgraphviz by E. Ganssner, S. North, www.graphviz.org
g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz", package="graph")) if(require(XML)) { g1 <- fromGXL(g1_gz) ag <- agopen(g1, name="test") toFile(ag, layoutType="dot", filename="g1_dot.svg", fileType="svg") toFile(ag, layoutType="neato", filename="g1_neato.ps", fileType="ps") toFile(ag, layoutType="twopi", filename="g1_twopi.svg", fileType="svg") }g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz", package="graph")) if(require(XML)) { g1 <- fromGXL(g1_gz) ag <- agopen(g1, name="test") toFile(ag, layoutType="dot", filename="g1_dot.svg", fileType="svg") toFile(ag, layoutType="neato", filename="g1_neato.ps", fileType="ps") toFile(ag, layoutType="twopi", filename="g1_twopi.svg", fileType="svg") }
This class is used to describe a coordinate in 2-dimensional (X/Y) space
Objects can be created by calls of the form new("xyPoint", ...).
x:Object of class "numeric" The x coordinate
y:Object of class "numeric" The y coordinate
Returns the value stored in the x slot
Returns the value stored in the y slot
Returns a vector of two numerical values
representing the x and y positions
Display information about the object in a concise fashion
Jeff Gentry
z <- new("xyPoint", x=150, y=30) z getPoints(z) getX(z) getY(z)z <- new("xyPoint", x=150, y=30) z getPoints(z) getX(z) getY(z)