xgobi

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XGobi: Dynamic Graphics for Data Analysis

Dynamic graphics, including brushing, rotation, grand tour, projection pursuit, slicing. Most effectively used when called more than once on same data, which then allows linked plots. Brushing with several glyphs and colors is supported. (On monochrome displays, only glyphs can be used.)

Keywords
multivariate, dynamic
Usage
xgobi(matrx, collab = colnames(matrx), rowlab = rownames(matrx), colors = NULL, glyphs = NULL, erase = NULL, lines = NULL, linecolors = NULL, resources = NULL, title = deparse(substitute(matrx)), vgroups = NULL, std = "mmx", nlinkable = NULL, subset = NULL, display = NULL, multi = TRUE, keep = FALSE, fprefix = "xgobi-")
xgobi.colors.default
Arguments
matrx
numeric n * p matrix or data.frame.
collab
character vector of p column labels (defaulting to those of matrx); if no default exists, xgobi constructs its own ("Var1",....).
rowlab
character vector of n row labels (defaulting to those of matrx); if no default exists, xgobi constructs its own (numbers 1:n).
colors
Optional character vector, used to supply initial point colors to be used; the default is that all points are the same color. Details, see below.
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.

Glyphs have been coming as six different types (plus, X, open and filled rectangle, open and filled circle) in five different sizes, plus ``point'', giving 31 available glyphs.

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. The default connecting line matrix connects each point to the one that follows it in the data; that is, (1 2), (2 3), (3 4), ..., (n-1, n).
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 XGobi was initiated during an R session).
title
Optional character string which defines the -title argument used by X. Defaults to the name (expression) of the current matrx argument. See documentation for xgobi, or for X.
vgroups
Optional integer vector, used to assign columns to groups for transformation and axis scaling. This vector must contain one integer for each variable. Columns to be grouped together should share the same integer. Default is the vector 1:(ncol(matrx)).
std
Optional string; which standardization of view to use. Default is "mmx", minimum-maximum scaling, in which the view is centered at the midpoint of the data, and all the data fits inside the plotting window. Alternatives are "msd", in which the plot is centered at the mean of the data, or "mmd" in which the plot is centered at the median. In those two cases, the view is standardized using the largest distance.
nlinkable
Optional integer scalar, the number of rows to be used in linking of brushing and identification; the default is for all rows to be used. This feature can be used to link ordinary scatterplots with plots that have some decorations requiring additional points, such as clustering trees.
subset
Optional integer scalar, the number of rows to be included in the initial display. That is, all data will be read in, but an initial random sample will be drawn for display. Use the Subset panel on the Tools Menu to select a new subset during the session.
display
Optional character string, identifying the monitor on which to display the xgobi window. The default is "machine:0.0" where machine is the name of the user's workstation. See documentation for xgobi or 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.
Details

xgobi.colors.default is the vector of the ten default brush colors from which to choose by the colors argument.

Note that this sef of default brush colors can be modified by a (site or user) specific ‘app-defaults’ file, or directly by xgobi(*, resources = ..), redefining (*brushColor$n$ (with $n$ from 0:9).

A warning is issued if colors contains strings not in the brushColor resources.

Value

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

Side Effects

The R function xgobi executes a call to the C program of the same name, an interactive statistical graphics program which runs under the X Window System, and returns control of the R command line to the user. XGobi can be used to create vectors of brushing information and rotation coefficients; see the documentation for XGobi for details.

CONTACT

(xgobi main program): D. F. Swayne dfs@research.att.com

References

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

See Also

xgvis which uses xgobi for interactive MDS.

Aliases
  • xgobi
  • xgobi.colors.default
Examples
data(laser)
xgobi(laser)

Xdir <- file.path(dirname(tempfile()), "xgobi")

dir.create(Xdir)
xgobi(laser, colors = xgobi.colors.default[c(1,3,5,7,9,10)[as.factor(laser$ Ir)]],
      glyphs = c(23,8)[1+(laser$lambda > 1576)],
      keep = TRUE, fprefix="xgobi/L-")
file.info(list.files(Xdir, full=TRUE))[, c(1,3,4)] # >> Files "L-laser..."
## remove manually when finally unused:
unlink(Xdir, recursive = TRUE)

##>>> see also the morsecodes example in  help(xgvis) <<<
##                 ------------------     -----------
Documentation reproduced from package xgobi, version 1.2-15, License: file LICENSE

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