distGraph-class {graph} | R Documentation

## Class "distGraph"

### Description

A class definition for graphs that are based on distances.

### Objects from the Class

Objects can be created by calls of the form `new("distGraph", ...)`.

### Slots

`Dist`:

  Object of class `"dist"` that forms the basis for the edge weights used in the `distGraph`.

### Extends

Class `"graph"`, directly.

### Methods

show

  `signature(object = "distGraph")`: a print method

Dist

  `signature(object = "distGraph")`: return the dist object.

adj

  `signature(object = "distGraph")`: find the nodes adjacent to the supplied node.

nodes

  `signature(object = "distGraph")`: return the nodes in the graph.

numNodes

  `signature(object = "distGraph")`: return the number of nodes.

threshold

  `signature(object = "distGraph", k, value)`: set all distances that are larger than the supplied threshold, `k`, to the supplied value. The default is value is zero (and so is appropriate for similarities, rather than distances).

initialize

  `signature(object = "distGraph")`: initialize a `distGraph` instance.

edgeWeights

  Return a list of edge weights in a list format similar to the `edges` method.

edgeL

  `signature(graph = "distGraph")`: A method for obtaining the edge list.

### Author(s)

R. Gentleman

### References

Shamir's paper and Butte et al

### See Also

`graph-class`, `clusterGraph-class`

### Examples

       set.seed(123)
       x <- rnorm(26)
       names(x) <- letters
       library(stats)
       d1 <- dist(x)
       g1 <- new("distGraph", Dist=d1)

[Package graph version 1.65.3 Index]