xgobi                 package:xgobi                 R Documentation

_X_G_o_b_i: _D_y_n_a_m_i_c _G_r_a_p_h_i_c_s _f_o_r _D_a_t_a _A_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

     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.)

_U_s_a_g_e:

     xgobi(matrx,
           collab = dimnames(matrx)[[2]],
           rowlab = dimnames(matrx)[[1]],
           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,
           keep = FALSE, fprefix = "xgobi-")

     xgobi.colors.default

_A_r_g_u_m_e_n_t_s:

   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.

    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.

_D_e_t_a_i_l_s:

     `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.

_V_a_l_u_e:

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

_S_i_d_e _E_f_f_e_c_t_s:

     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.

_C_O_N_T_A_C_T:

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

_A_u_t_h_o_r(_s):

     of R port: Kurt Hornik and Martin Maechler
     maechler@stat.math.ethz.ch

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     `xgvis' which uses `xgobi' for interactive MDS.

_E_x_a_m_p_l_e_s:

     data(laser)
     xgobi(laser)

     system("mkdir /tmp/xgobi")
     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-")
     system("ls -l /tmp/xgobi")# >> Files "L-laser..."
     ## remove manually when finally unused:
     system("rm /tmp/xgobi/L-*")

     ##>>> see also the morsecodes example in  help(xgvis) <<<
     ##                 ------------------     -----------

