R: Multi-dimensional Scaling Plot of Proximity matrix from RRF

MDSplot {RRF} | R Documentation

## Multi-dimensional Scaling Plot of Proximity matrix from RRF

### Description

Plot the scaling coordinates of the proximity matrix from RRF.

### Usage

    MDSplot(rf, fac, k=2, palette=NULL, pch=20, ...)

### Arguments

`rf` | an object of class `RRF` that contains the `proximity` component.
`fac` | a factor that was used as response to train `rf`.
`k` | number of dimensions for the scaling coordinates.
`palette` | colors to use to distinguish the classes; length must be the equal to the number of levels.
`pch` | plotting symbols to use.
`...` | other graphical parameters.

### Value

The output of `cmdscale` on 1 - `rf$proximity` is returned invisibly.

### Note

If `k > 2`, `pairs` is used to produce the scatterplot matrix of the coordinates.

### Author(s)

Robert Gentleman, with slight modifications by Andy Liaw

### See Also

`RRF`

### Examples

    set.seed(1)
    data(iris)
    iris.rf <- RRF(Species ~ ., iris, proximity=TRUE,
                            keep.forest=FALSE)
    MDSplot(iris.rf, iris$Species)
    ## Using different symbols for the classes:
    MDSplot(iris.rf, iris$Species, palette=rep(1, 3), pch=as.numeric(iris$Species))

[Package RRF version 1.9.4 Index]