R: Plotting Distance Matrices (wordspace)

plot.dist.matrix {wordspace} | R Documentation

## Plotting Distance Matrices (wordspace)

### Description

Visualization of a DSM distance matrix as a neighbourhood graph based on multidimensional scaling (MDS).

### Usage

      ## S3 method for class 'dist.matrix'
    plot(x, y, labels=rownames(x), show.labels=TRUE, label.pos=3,
         selected=attr(x, "selected"), show.selected=TRUE,
         col="black", cex=1, pch=20, pt.cex=1.2, selected.cex=1.2, selected.col="red",
         show.edges=TRUE, edges.lwd=6, edges.col="#AABBFF", edges.threshold=quantile(x, 2/3),
         method=c("isomds", "sammon"), aspect=1, expand=.05, ...)

### Arguments

`x` | a symmetric distance matrix of class `dist.matrix`. NB: similarity values and asymmetric distance measures are not supported.
`y` | unused, must not be specified
`labels` | a character vector of labels for the DSM vectors (defaults to rownames of `x`)
`show.labels` | if `TRUE` (default), labels are displayed if available
`label.pos` | position of labels (default: above points). Possible values are `1` (below), `2` (left), `3` (above) and `4` (right).
`selected` | logical vector of selected points that will be highlighted (defaults to optional `selected` attribute of distance matrix)
`show.selected` | if `TRUE` (default), points marked by `selected` are highlighted in the plot
`col` | colour of points and labels
`cex` | numeric character expansion factor for points and labels
`pch` | plot symbol for points
`pt.cex` | character expansion factor for points relative to labels
`selected.cex` | additional character expansion factor for selected points and labels
`selected.col` | colour of selected points and labels (if `show.selected=TRUE`)
`show.edges` | if `TRUE` (default), edges are drawn between points. The line width of each edge is proportional to the distance between the corresponding points.
`edges.lwd` | maximal line width of edges (for d = 0)
`edges.col` | colour of edges, usually a light or translucent shade
`edges.threshold` | maximal distance up to which edges are drawn. The default is to display two thirds of all edges.
`method` | whether to perform non-metric (`isomds`) or metric (`sammon`) multidimensional scaling
`aspect` | aspect ratio of plot window (e.g. `aspect=16/10` for a window that is 8 inches wide and 5 inches high). Setting a correct aspect ratio ensures that the distances between points in the MDS map are correctly represented in the plot.
`expand` | fraction by which plotting region is extended on each side. Adjust this parameter so that points and labels are completely visible.
`...` | all other arguments are passed to the initial plot function, which sets up the display but does not draw any graphical elements

### Details

For multidimensional scaling (MDS), the functions `isoMDS` and `sammon` from the MASS package are used.

### Value

Invisibly returns a two-column matrix with MDS coordinates of all displayed points and `labels` as rownames (if available).

### Author(s)

Stefan Evert (http://purl.org/stefan.evert)

### See Also

`nearest.neighbours`, which produces distance matrices suitable for plotting if the option `dist.matrix=TRUE` is specified

### Examples

    ## Not run:
    plot(nearest.neighbours(DSM_Vectors, "walk_V", n=20, dist.matrix=TRUE))

    ## End(Not run)

[Package wordspace version 0.2-6 Index]