xgvis: interactive multidimensional scaling using xgobi for display

Usage

xgvis(matrx,
edges=NULL, pos=NULL, rowlab=NULL, colors=NULL, glyphs=NULL,
erase=NULL, lines=NULL, linecolors=NULL, resources=NULL,
display=NULL)

Arguments

matrx An nxn distance matrix
edges Line segments: specifications for the pattern of line segments which connect pairs of points. The file 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 fname.lines file in xgobi.) In addition, if a third number is present, it is taken to be an edge weight. If this line is present and the distance matrix is absent, then the distance matrix is computed from it, with each edge representing a distance of one.
pos Starting positions: an n x p matrix, with entries separated by white space and one row per line. If this file is present and a distance file is absent, the distance matrix is computed from it.
rowlab Optional character vector of row labels; the default is dimnames(matrx)[[1]]. If no default exists, xgobi constructs its own defaults.
colors Optional character vector, used to supply initial point colors to be used; the default is that all points are the same color.
glyphs Optional integer vector, used to supply glyphs to be used on startup; the default is that all points are drawn with the same glyph.
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 this file is present, then the edges file is used to create the distance matrix but the lines file 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 (if this XGvis was initiated during an S session).
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.

Description

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.

Value

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

Side Effects

The xgvis S function executes a call to the C program of the same name, and returns control of the S shell to the user.

CONTACT

D. F. Swayne dfs@research.att.com

References

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

Examples

## The following examples use sample data files from the data_xgvis
## directory in the xgobi and xgvis distribution directory.

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

data(perm4)
xgvis(edges = perm4.edges)
xgvis(edges = perm4.edges,
      linecolors = perm4.linecolors)


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