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jmc |
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\name{classesToAM}
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murdoch |
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\alias{classesToAM}
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jmc |
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\title{
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murdoch |
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Compute an Adjacency Matrix for Superclasses of Class Definitions
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jmc |
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}
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\description{
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Given a vector of class names or a list of class definitions, the
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function returns an adjacency matrix of the superclasses of these
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classes; that is, a matrix with class names as the row and column
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names and with element [i, j] being 1 if the class in column j is a
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direct superclass of the class in row i, and 0 otherwise.
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The matrix has the information implied by the \code{contains} slot of
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the class definitions, but in a form that is often more convenient for
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further analysis; for example, an adjacency matrix is used in packages
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and other software to construct graph representations of relationships.
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}
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\usage{
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classesToAM(classes, includeSubclasses = FALSE,
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abbreviate = 2)
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}
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\arguments{
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\item{classes}{
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Either a character vector of class names or a list, whose
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elements can be either class names or class definitions. The
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list is convenient, for example, to include the package slot for
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the class name. See the examples.
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}
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\item{includeSubclasses}{
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A logical flag; if \code{TRUE}, then the matrix will include all
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the known subclasses of the specified classes as well as the
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superclasses. The argument can also be a logical vector of the
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same length as \code{classes}, to include subclasses for some
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but not all the classes.
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}
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\item{abbreviate}{
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Control of the abbreviation of the row and/or column labels of
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the matrix returned: values 0, 1, 2, or 3 abbreviate neither,
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rows, columns or both. The default, 2, is useful for printing
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the matrix, since class names tend to be more than one
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character long, making for spread-out printing. Values of 0
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or 3 would be appropriate for making a graph (3 avoids the
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tendency of some graph plotting software to produce labels in
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minuscule font size).
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}
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}
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\details{
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For each of the classes, the calculation gets all the superclass
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names from the class definition, and finds the edges in those classes'
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definitions; that is, all the superclasses at distance 1. The
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corresponding elements of the adjacency matrix are set to 1.
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The adjacency matrices for the individual class definitions are
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merged. Note two possible kinds of inconsistency, neither of which
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should cause problems except possibly with identically named classes from
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different packages. Edges are computed from each superclass
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definition, so that information overrides a possible inference from
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extension elements with distance > 1 (and it should). When
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matrices from successive classes in the argument are merged, the
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computations do not currently check for inconsistencies---this is
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the area where possible multiple classes with the same name could
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cause confusion. A later revision may include consistency checks.
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}
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\value{
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As described, a matrix with entries 0 or 1, non-zero values
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indicating that the class corresponding to the column is a direct
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superclass of the class corresponding to the row. The row and
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column names are the class names (without package slot).
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}
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\seealso{
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\code{\link{extends}} and \linkS4class{classRepresentation} for the underlying information from the class
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definition.
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}
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\examples{
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ripley |
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## the super- and subclasses of "standardGeneric"
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## and "derivedDefaultMethod"
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jmc |
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am <- classesToAM(list(class(show), class(getMethod(show))), TRUE)
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am
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\dontrun{
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## the following function depends on the Bioconductor package Rgraphviz
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plotInheritance <- function(classes, subclasses = FALSE, ...) {
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if(!require("Rgraphviz", quietly=TRUE))
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stop("Only implemented if Rgraphviz is available")
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mm <- classesToAM(classes, subclasses)
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classes <- rownames(mm); rownames(mm) <- colnames(mm)
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graph <- new("graphAM", mm, "directed", ...)
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plot(graph)
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cat("Key:\n", paste(abbreviate(classes), " = ", classes, ", ",
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sep = ""), sep = "", fill = TRUE)
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invisible(graph)
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}
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## The plot of the class inheritance of the package "graph"
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require(graph)
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plotInheritance(getClasses("package:graph"))
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}
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}
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\keyword{classes}
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\keyword{programming}
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