Package 'classGraph'

The R Package 'classGraph'

Description

The package classGraph is package using graph and graph visualization methods to visualize inheritance graphs of S4 classes.

Details

Package:	classGraph
Type:	Package
Title:	Construct Graphs of S4 Class Hierarchies
Version:	0.7-6
Author:	Martin Maechler partly based on code from Robert Gentleman
Maintainer:	Martin Maechler <[email protected]>
Depends:	methods
Imports:	graphics, stats, utils, graph, Rgraphviz
Suggests:	Matrix
Description:	Construct directed graphs of S4 class hierarchies and visualize them. In general, these graphs typically are DAGs (directed acyclic graphs), often simple trees in practice.
License:	GPL
NeedsCompilation:	no
Packaged:	2023-08-21 16:31:10 UTC; maechler
Date/Publication:	2023-08-21 19:50:02 UTC
Repository:	https://mmaechler.r-universe.dev
RemoteUrl:	https://github.com/cran/classGraph
RemoteRef:	HEAD
RemoteSha:	1666954776a5334a49c621fd733e1aadebd953ec

Index of help topics:

bGraph                  Create a "Branch Graph" (Simple Tree with Root
                        and Leaves)
class2Graph             Build the Graph of Super Classes from an S4
                        Class Definition
classGraph-package      The R Package 'classGraph'
classTree               builds a directed graph, typically a tree from
                        a class Object
mRagraph                Construct a Laid-Out Graph for Plotting
numOutEdges             For each Node of a Directed Graph give the
                        Number Outgoing Edges
plotRag                 Plot an Ragraph (using Rgraphviz)
subClasses              All Subclasses of a Given S4 Class
superClasses            List of Super Classes of a Given S4 Class

Author(s)

Martin Maechler

See Also

classTree() is the main function of this package.

---

Create a "Branch Graph" (Simple Tree with Root and Leaves)

Description

Create a “Branch Graph”, i.e., a simple tree with root and $n$ (simple) branches or leaves.

Usage

bGraph(n, root = "Mom",
       leaves = paste(l.prefix, seq(length = n), sep = ""),
       l.prefix = "D", weights = NULL,
       mode = c("undirected", "directed"))

Arguments

n	integer specifying the number of leave branches.
root	the node on which to root the tree.
leaves	the nodes to be used as leaves.
l.prefix	a string specifying .....
weights	.......
mode	string indicating which mode is to be used.

Value

a graph object of class graphNEL.

Author(s)

Martin Maechler, Aug.2005

See Also

class graphNEL; ftM2graphNEL.

Examples

require("graph") ## Using package 'graph' => plot() method (via package 'Rgraphviz'):

(bg7 <- bGraph(7)) # 8 nodes {Mom, D1..D7}; 7 edges
plot(bg7) # draws the graph

(bgD3 <- bGraph(3, mode="directed"))
plot(bgD3) # directed: using arrows

(bgw2 <- bGraph(2, weights = c(10,1)))
plot(bgw2) # {maybe use lwd for weights in the future?}
if(require("Matrix"))
  show(as(bgw2, "sparseMatrix")) # shows the weights

---

Build the Graph of Super Classes from an S4 Class Definition

Description

From an S4 class definition class, computes the graph of all super classes, i.e., of all classes that class extends.

Usage

class2Graph(class, fullNames = TRUE, simpleOnly = FALSE,
            bottomUp = FALSE, package = class@package)

Arguments

class	class name
fullNames	logical indicating if full name should be applied....
simpleOnly	logical, simply passed to getAllSuperClasses(..).
bottomUp	logical indicating the direction of the graph.
package	package where the super classes should be gotten from.

Value

an R object inheriting from class graph.

Author(s)

Robert Gentleman (original code) and Martin Maechler

See Also

classTree which builds the graph of all subclasses.

Examples

require("graph")
cg <- class2Graph("graphNEL") # simple :  graphNEL |-> graph
plot(cg)

if(require("Matrix")) {
   cg2 <- class2Graph("dgCMatrix")
   as(cg2, "sparseMatrix")
   plot(cg2)
   ## alternative: don't show the initial "Matrix:"
   cg2. <- class2Graph("dgCMatrix", fullNames=FALSE)
   plot(cg2.)
   ## 'simpleOnly' does not change anything here :
   stopifnot(identical(cg2.,
          class2Graph("dgCMatrix", fullNames=FALSE, simpleOnly = TRUE)))


   ## very simple, since "sparseMatrix" only extends "Matrix" :
   cg3 <- class2Graph("sparseMatrix")
   plot(cg3)
}

---

builds a directed graph, typically a tree from a class Object

Description

From an S4 class, by investigating all subclasses, a inheritance graph is built, a directed graph, often a tree.

Usage

classTree(Cl, all = FALSE, ...)

Arguments

Cl	class name ...
all	logical indicating if all instead of just direct sub-classes should be used.
...	....

Value

an R object inheriting from class graph.

Author(s)

Martin Maechler

See Also

class2Graph, ...

Examples

## Using classes and methods from package 'graph' :
trGclass <- classTree("graph")
as(trGclass, "matrix")
plot(trGclass) # using package 'Rgraphviz'

---

Construct a Laid-Out Graph for Plotting

Description

My constructor of an Ragraph object, a kind of “laid-out” graph, from package Rgraphviz. This allows more customization in plotting than just calling plot(gr, ...) for a graph object from package graph.

Usage

mRagraph(gr, lType, fixedsize = FALSE,
         fill = c("lightblue", "gray90"),
         color = c("blue3", "gray60"),
         labcol = c("blue3", "green4", "purple"))

Arguments

gr	an R object of class graph (from package graph), in our case typically the result of classTree().
lType	a string specifying the layout type, see agopen() in package Rgraphviz for the possibilities.
fixedsize	logical indicating if the ellipses should all get the same size – or should rather adapt to the situation.
fill	character vector of length 2....
color	character vector of length 2....
labcol	vector of labels to be used ....

Value

an object of class Ragraph, produced by an appropriate call to agopen.

Author(s)

Martin Maechler

See Also

the customized plotting function plotRag.

Examples

if(require("Matrix")) {
    trMatrix <- classTree("Matrix")
    trMatrix
    RtrM <- mRagraph(trMatrix)
    RtrM # (the show method will hopefully improve)
    str(RtrM, max=2) # shows a bit more

    plot(RtrM)# 'graph' method -> using 'Rgraphviz' package
  }

---

For each Node of a Directed Graph give the Number Outgoing Edges

Description

In a directed or undirected graph, for each node count the number of edges “leaving” that nodes.

Usage

numOutEdges(g)

Arguments

g	an R object of class graph (from package graph).

Value

an integer vector the same length as nodes(g) giving the number of edges that “go out” from each node.

Author(s)

Martin Maechler

See Also

edgeL on which this function is built, and leaves, both from package graph.

Examples

## Simplistic leaves() definition for *directed graphs* :
## { compare with graph::leaves() }
is.leaf <- function(g) numOutEdges(g) == 0 ## (also exists hiddenly..)
Leaves  <- function(g) graph::nodes(g)[is.leaf(g)]
Leaves(bGraph(4, mode = "directed"))

---

Plot an Ragraph (using Rgraphviz)

Description

Plot an Ragraph object (a kind of “laid-out” graph, from package Rgraphviz). This the simply uses the plot method from package Rgraphviz (i.e., selectMethod(plot, "Ragraph")) and additionally adds a “footnote”-like subtitle.

Usage

plotRag(ragr, sub, subArgs = .optRagargs(), ...)

.optRagargs(side = 1, adj = 0.05, cex = 0.75, line = 3)

Arguments

ragr	an object of class Ragraph (as defined in the Rgraphviz package).
sub	a “footnote” or subtitle to be added to plot(ragr,...). By default gives the number of nodes and edges.
subArgs	a list of arguments to mtext, typically from calling .optRagargs().
...	further arguments passed to plot(.), i.e., the plot method for Ragraph objects.
side, adj, cex, line	arguments passed to mtext() with non-standard defaults in order to place sub, the “sub title”.

Author(s)

Martin Maechler

See Also

mRagraph, Ragraph.

Examples

if(require("Matrix")) {
    trMatrix <- classTree("Matrix")
    trMatrix
    RtrM <- mRagraph(trMatrix)
    RtrM # (the show method will hopefully improve)
    str(RtrM, max=2) # shows a bit more

    plot(RtrM) ## almost the same as
    plotRag(RtrM, subArgs=.optRagargs(adj = 0.5))
               ## which just gives "<n> nodes with <m> edges"
  }

---

All Subclasses of a Given S4 Class

Description

Retugn all subclasses of a given S4 class; either only the direct sub classes are also those “further away” (distance $> 1$).

Usage

subClasses(Cl, directOnly = TRUE, complete = TRUE, ...)

Arguments

Cl	a class representation or a class name (character).
directOnly	logical indicating if you direct subclasses are desired (or also the ones with distance $> 1$).
complete	logical,.. as in....
...	........

Value

a character vector of class names.

Author(s)

Martin Maechler

See Also

superClasses; Classes in general.

Examples

subClasses("graph") # -> the direct ones
subClasses("graph", directOnly = FALSE) # the same: has only direct subclasses
if(require("Matrix")) {
  print( subClasses("sparseMatrix") )
  print( subClasses("sparseMatrix", directOnly = FALSE) )# much more
}

---

List of Super Classes of a Given S4 Class

Description

Give a list of all super classes of a specific S4 class (definition).

Usage

superClasses(x)

Arguments

x	a class representation as returned by getClassDef.

Value

a list of length-1 character strings, typically with a "package" attribute each.

Author(s)

Robert Gentleman and Martin Maechler

See Also

subClasses, ...

Examples

superClasses(getClassDef("graphNEL"))

if(require("Matrix")) {
  scL <- superClasses(getClassDef("dgeMatrix"))
  str(scL) # a list of two
} # 'Matrix'

---