R: Plot of a Partition of the Data Set

plot.partition {cluster} | R Documentation

## Plot of a Partition of the Data Set

### Description

Creates plots for visualizing a `partition` object.

### Usage

    ## S3 method for class 'partition'
    plot(x, ask = FALSE, which.plots = NULL,
         nmax.lab = 40, max.strlen = 5, data = x$data, dist = NULL,
         stand = FALSE, lines = 2,
         shade = FALSE, color = FALSE, labels = 0, plotchar = TRUE,
         span = TRUE, xlim = NULL, ylim = NULL, main = NULL, ...)

### Arguments

`x` | an object of class `"partition"`, typically created by the functions `pam`, `clara`, or `fanny`.
`ask` | logical; if true and `which.plots` is `NULL`, `plot.partition` operates in interactive mode, via `menu`.
`which.plots` | integer vector or NULL (default), the latter producing both plots. Otherwise, `which.plots` must contain integers of `1` for a clusplot or `2` for silhouette.
`nmax.lab` | integer indicating the number of labels which is considered too large for single-name labeling the silhouette plot.
`max.strlen` | positive integer giving the length to which strings are truncated in silhouette plot labeling.
`data` | numeric matrix with the scaled data; per default taken from the partition object `x`, but can be specified explicitly.
`dist` | when `x` does not have a `diss` component as for `pam(*, keep.diss=FALSE)`, `dist` must be the dissimilarity if a clusplot is desired.
`stand,lines,shade,color,labels,plotchar,span,xlim,ylim,main, ...` | All optional arguments available for the `clusplot.default` function (except for the `diss` one) and graphical parameters (see `par`) may also be supplied as arguments to this function.

### Details

When `ask= TRUE`, rather than producing each plot sequentially, `plot.partition` displays a menu listing all the plots that can be produced. If the menu is not desired but a pause between plots is still wanted, call `par(ask= TRUE)` before invoking the plot command.

The clusplot of a cluster partition consists of a two-dimensional representation of the observations, in which the clusters are indicated by ellipses (see `clusplot.partition` for more details).

The silhouette plot of a nonhierarchical clustering is fully described in Rousseeuw (1987) and in chapter 2 of Kaufman and Rousseeuw (1990). For each observation i, a bar is drawn, representing its silhouette width s(i), see `silhouette` for details. Observations are grouped per cluster, starting with cluster 1 at the top. Observations with a large s(i) (almost 1) are very well clustered, a small s(i) (around 0) means that the observation lies between two clusters, and observations with a negative s(i) are probably placed in the wrong cluster.

A clustering can be performed for several values of `k` (the number of clusters). Finally, choose the value of `k` with the largest overall average silhouette width.

### Side Effects

An appropriate plot is produced on the current graphics device. This can be one or both of the following choices:
Clusplot
Silhouette plot

### Note

In the silhouette plot, observation labels are only printed when the number of observations is less than `nmax.lab` (40, by default), for readability. Moreover, observation labels are truncated to maximally `max.strlen` (5) characters.
For more flexibility, use `plot(silhouette(x), ...)`, see `plot.silhouette`.

### References

Rousseeuw, P.J. (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math., 20, 53–65.

Further, the references in `plot.agnes`.

### See Also

`partition.object`, `clusplot.partition`, `clusplot.default`, `pam`, `pam.object`, `clara`, `clara.object`, `fanny`, `fanny.object`, `par`.

### Examples

    ## generate 25 objects, divided into 2 clusters.
    x <- rbind(cbind(rnorm(10,0,0.5), rnorm(10,0,0.5)),
               cbind(rnorm(15,5,0.5), rnorm(15,5,0.5)))
    plot(pam(x, 2))

    ## Save space not keeping data in clus.object, and still clusplot() it:
    data(xclara)
    cx <- clara(xclara, 3, keep.data = FALSE)
    cx$data # is NULL
    plot(cx, data = xclara)

[Package cluster version 2.1.0 Index]