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classesToAM: Compute an Adjacency Matrix for Superclasses of Class...

classesToAM

R Documentation

Compute an Adjacency Matrix for Superclasses of Class Definitions

Description

Given a vector of class names or a list of class definitions, the function returns an adjacency matrix of the superclasses of these classes; that is, a matrix with class names as the row and column names and with element [i, j] being 1 if the class in column j is a direct superclass of the class in row i, and 0 otherwise.

The matrix has the information implied by the contains slot of the class definitions, but in a form that is often more convenient for further analysis; for example, an adjacency matrix is used in packages and other software to construct graph representations of relationships.

Usage

classesToAM(classes, includeSubclasses = FALSE,
       abbreviate = 2)

Arguments

`classes`	Either a character vector of class names or a list, whose elements can be either class names or class definitions. The list is convenient, for example, to include the package slot for the class name. See the examples.
`includeSubclasses`	A logical flag; if `TRUE`, then the matrix will include all the known subclasses of the specified classes as well as the superclasses. The argument can also be a logical vector of the same length as `classes`, to include subclasses for some but not all the classes.
`abbreviate`	Control of the abbreviation of the row and/or column labels of the matrix returned: values 0, 1, 2, or 3 abbreviate neither, rows, columns or both. The default, 2, is useful for printing the matrix, since class names tend to be more than one character long, making for spread-out printing. Values of 0 or 3 would be appropriate for making a graph (3 avoids the tendency of some graph plotting software to produce labels in minuscule font size).

Details

For each of the classes, the calculation gets all the superclass names from the class definition, and finds the edges in those classes' definitions; that is, all the superclasses at distance 1. The corresponding elements of the adjacency matrix are set to 1.

The adjacency matrices for the individual class definitions are merged. Note two possible kinds of inconsistency, neither of which should cause problems except possibly with identically named classes from different packages. Edges are computed from each superclass definition, so that information overrides a possible inference from extension elements with distance > 1 (and it should). When matrices from successive classes in the argument are merged, the computations do not currently check for inconsistencies—this is the area where possible multiple classes with the same name could cause confusion. A later revision may include consistency checks.

Value

As described, a matrix with entries 0 or 1, non-zero values indicating that the class corresponding to the column is a direct superclass of the class corresponding to the row. The row and column names are the class names (without package slot).

Examples


## the super- and subclasses of "standardGeneric"
## and "derivedDefaultMethod"
am <- classesToAM(list(class(show), class(getMethod(show))), TRUE)
am

## Not run: 
## the following function depends on the Bioconductor package Rgraphviz
plotInheritance <- function(classes, subclasses = FALSE, ...) {
    if(!require("Rgraphviz", quietly=TRUE))
      stop("Only implemented if Rgraphviz is available")
    mm <- classesToAM(classes, subclasses)
    classes <- rownames(mm); rownames(mm) <- colnames(mm)
    graph <-  new("graphAM", mm, "directed", ...)
    plot(graph)
    cat("Key:\n", paste(abbreviate(classes), " = ", classes, ", ",
        sep = ""),  sep = "", fill = TRUE)
    invisible(graph)
}

## The plot of the class inheritance of the package "graph"
require(graph)
plotInheritance(getClasses("package:graph"))


## End(Not run)