xgobi (version 1.2-15)

xgvis: XGvis: Interactive Multidimensional Scaling Using XGobi for Display

Description

R interface to XGvis, an interactive multidimensional scaling (MDS) program that consists of a control panel to manipulate the parameters of the MDS stress function and an xgobi window for data display. It can be used either for visualization of dissimilarity data, for dimension reduction, or for graph layout. Graph layout is usually done in 2D, but xgvis allows layouts in arbitrary dimensions, 3D being the default. It permits missing values, which can be used to implement multidimensional unfolding.

Usage

xgvis(dmat = NULL, edges= NULL, pos  = NULL, rowlab = colnames(dmat), colors = NULL, glyphs = NULL, erase = NULL, lines = NULL, linecolors = NULL, resources = NULL, display = NULL, multi = TRUE, keep = FALSE, fprefix = "xgvis-")

Arguments

dmat

numeric $n * n$ distance matrix.

edges

$n * 2$ or $n * 3$ matrix of specifications for the pattern of line segments which connect pairs of points. Must contain at least two numbers per line. The first two numbers represent the row numbers of the two points that should be connected. (This is exactly like the structure of a the lines argument of xgobi.) In addition, if a third number is present, it is taken to be an edge weight.

If edges is specified and dmat not, then the distance matrix is computed from edges, with each edge representing a distance of one.

pos

Starting positions: an n * p matrix. If pos is specified and dmat not, the distance matrix is computed from pos.

rowlab

character vector of n row labels (defaulting to those of dmat); if no default exists, xgobi constructs its own (numbers 1:n).

colors

optional character vector supplying initial point colors to be used; see xgobi.

glyphs

integer vector, used to supply glyphs to be used on startup, see xgobi.

erase

Optional integer vector of length equal to the number of rows in the data and composed of 1s and 0s. A 1 in position i specifies that point i should be erased. The default is a vector of 0s.

lines

Optional integer matrix, n by 2, which specifies by row number pairs of points to be connected by line segments. If lines are specified, then the edges is used to create the distance matrix but lines is used to draw the edges.

linecolors

Optional integer vector, of length n where n is the number of lines specified by the lines argument. It is used to supply line colors to be used on startup; the default is for all the lines to be drawn in the standard foreground color.

resources

Optional character vector created by clicking on the ``Save Resources'' button in XGobi.

display

Optional character string, identifying the monitor on which to display the xgvis window. The default is "machine:0.0" where machine is the name of the user's workstation. See documentation for X.

multi

logical, indicating if the xgobi process should be run multi-tasking with R. If true, control returns to the R command prompt after 3 seconds.

keep

logical, indicating if the temporary files should be kept (e.g. for calling the xgobi program outside R)

fprefix

character string for the file name prefix to be used for temporary files.

Value

The UNIX status upon completion, i.e. 0 if ok.

Side Effects

The xgvis R function executes a call to the C program of the same name, and returns control of the R command line to the user.

CONTACT

D. F. Swayne

References

http://www.research.att.com/areas/stat/xgobi/, http://www.public.iastate.edu/~dicook/

See Also

xgobi.

Examples

data(morsecodes) ## from the XGobi/XGvis data, see  ?morsecodes
mc.row <- paste(morsecodes.row[,1],morsecodes.row[,2])

xgvis(dmat = morsecodes.dist,
      pos = morsecodes.pos,
      rowlab = mc.row,
      colors = morsecodes.colors,
      glyphs = morsecodes.glyphs,
      lines = morsecodes.lines,
      linecolors = morsecodes.linecolors)

##>   2) Show lines by hitting "l" with the mouse over the plot.
##>   3) Examine morsecode labels by hitting "i" and mousing around on the plot.
##>   3b) Press "r" (on the plot) to switch 3D rotation in xgobi.
##>   4) Run MDS in 3D by clicking "Run MDS" (in xgvis).
##>   5) Speed up the optimization by increasing the "Stepsize" with the slider.
##>      The "Stress function" value may go as low as 0.1925 (MM).
##>   6) When the optimization calms down, click "Run MDS" to toggle MDS off.
##>   7) Rotate the MDS configuration in 3D {by "r" with mouse over plot}.
##>   8) Increase the rotation speed with the slider in the top left and
##>      control the rotation direction by dragging the mouse on the plot.
##>   9) You can check out the initial configuration by

## In order to have no color warning :
Mcolors <- unique(morsecodes.colors)
(Mcolors <- paste("*brushColor", 0:(length(Mcolors)-1),": ", Mcolors, sep=""))

xgobi(morsecodes.pos, collab = morsecodes.col, rowlab = mc.row,
      colors = morsecodes.colors,
      glyphs = morsecodes.glyphs,
      lines  = morsecodes.lines,
      linecolors = morsecodes.linecolors,
      resources= c("*showLines: True", Mcolors))

##>      This XGobi window will be linked with
##>      the XGvis window for glyph-color brushing and labeling.