NAME
          xgobi - interactive dynamic graphics program for data visu-
          alization

     SYNOPSIS
          xgobi [ X options ] [ -subset n ] [ -mono ] [ -version ] [
          -std mmx|msd|mmd ] [ -dev std_deviation ] filename

     DESCRIPTION
          xgobi is an interactive dynamic graphics program for data
          visualization in the X Window System.  It is especially
          designed for the exploration of multivariate data.  Its
          basic plot is a scatterplot, and these are some of the tools
          available for scatterplot display and manipulation:

            o Cycling rapidly through two-variable scatter plots.

            o Three-dimensional rotation, including trackball control,
              in spaces spanned by three variables at a time.

            o Grand tours and correlation tours: smooth randomized
              sequences of two-dimensional projections in order to
              explore a higher-dimensional point cloud of multivariate
              data.  Projections can be manually controlled and opti-
              mized with projection pursuit.

            o Brushing: the ability to change the color or plotting
              character of a point or a group of points.

            o Scaling: moving and reshaping the plot interactively.

            o Identification: displaying a label next to a point in
              the plot window.

            o Linked views: Brushing, identification and touring are
              linked; that is, actions in the window of one XGobi pro-
              cess are immediately reflected in another XGobi window
              displaying the same data.

            o Line editing: Any pair of points can be connected with a
              line segment.

            o Moving points:  Points can be moved on the screen.  In
              higher-dimensional views, the motion is interpreted as
              taking place in some plane parallel to the screen.

            o Smooths: Smooth curves can be drawn through point
              clouds.

            o Subsetting: Subsamples can be drawn either systemati-
              cally or randomly.

            o Jittering: Variables can be jittered, which is useful
              for discrete variables that take on only few values.

            o Parallel coordinate display: can be shown in a separate
              linked window, linked to the main window.

            o Case label list: can be shown in a separate window,
              linked to the main window for labeling points.

            o Missing values: are accepted and can be dealt with by
              imputation of constant values, random values, or user-
              supplied imputed values.  Missing value patterns can be
              examined in a separate linked XGobi window.

            o Variable transformations: A menu of transformations such
              as logs and a few powers is available.

            o Postscript plotting: The contents of the plot windows
              can be written out to postscript files for high-quality
              plotting.

            o Online help: Most of the XGobi buttons and windows have
              associated help files that can be displayed during an
              XGobi session.  Click on the Info button toward the top
              right of the window for instructions.

          XGobi has a direct manipulation interface, and all the above
          actions are performed using the mouse.

          XGobi can be used in conjunction with the S language for
          scientific computing and data analysis.  Execute help(xgobi)
          within S or Splus for information; if the xgobi function has
          not been installed, investigate the XGobi distribution
          files.

          XGobi can also be programmed to use RPC (Remote Procedure
          Calls) to communicate with other software.


     OPTIONS
          -subset n

            Specify the size n of the random sample of the data to be
            displayed on startup.  Although only the random sample is
            shown, all the data is read in and available during the
            session.  Use the subset panel in Tools to change the sam-
            ple size and sampling method during the session.

          -std mmx|msd|mmd

            By default, the data are scaled into the plotting window
            using the minimum and maximum values of each variable or
            variable group, in such a way that the midpoint of the
            variable is at the center of the plotting window and no
            points fall outside the window.  Instead, to scale using
            mean and standard deviation, specify -std msd; to scale
            using the median and median absolute deviation, specify
            -std mmd.

          -dev x

            If you have specified -std msd or -std mmd, then you can
            also specify the number of standard deviations (or median
            absolute deviations) from the mean (or median) to be con-
            tained within the plotting window, using the argument -dev
            x, where x is a real number between 0 and 100.  The
            default is 2.

          -mono

            Emulate a black-and-white display.  This simplifies pro-
            ducing pictures for many publications.

          -version

            Print a version date, the last date that any file in the
            release was changed.

          X options

            The standard X command line options can be used with
            XGobi.  These include -display machinename:0, used when
            running an X program on one machine and displaying its
            output on another, and -title Title, where Title is a
            string you want to appear in the window manager titlebar.

     FILES
          XGobi accepts standard input, but is most often used with
          files, partly because of the additional plot control that
          can be achieved using a set of files.  The data input file
          should be an ASCII file with the data matrix arranged in
          rows and columns; in ASCII, rows must be distinguished by
          carriage returns, and columns can be separated by any amount
          of white space.  Missing values can be coded as ".", "NA" or
          "na".  (The input file can also be a binary file, which can
          be produced within XGobi once the ASCII data has been read
          in.)  XGobi accepts other input about the display of the
          data from files as well.  If the data is in a file named

          filename

            or

          filename.dat
            (either of which must be an ASCII file), or

          filename.bin

            (the binary version of the data), then the other files are
            as follows:

          filename.row
          filename.rowlab
          filename.case

            Row or case labels: a label for each row of the data
            matrix, which is displayed in the identification mode.
            The file should contain one label per line.


          filename.col
          filename.collab
          filename.column
          filename.var

            Column or variable labels: a label for each column of the
            data matrix, which becomes part of the XGobi variable
            selection panel.  The file should contain one label per
            line.

          filename.colors

            Brushing colors: a color for each point in the plot, rep-
            resenting a row or case of the data.  The file should con-
            tain one color per line.  (It is probably best if the col-
            ors correspond to the colors used in brushing; see the
            later section on resources.)

          filename.glyphs

            Brushing glyphs: a glyph type for each point in the plot,
            representing a row or case of the data.  The file should
            contain one glyph type per line.  The glyph types are as
            follows:

               1 through 5: Five sizes of '+'
               6 through 10: Five sizes of 'X'
               11 through 15: Five sizes of open rectangle
               16 through 20: Five sizes of filled rectangle
               21 through 25: Five sizes of open circle
               26 through 30: Five sizes of filled circle
               31: A single-pixel point

          filename.erase

            Erase: a column of 1s (to have a point erased on startup)
            and 0s (to have the point plotted).  There should be one
            value per line and as many lines as there are rows in the
            data.

          filename.lines

            Line segments: specifications for the pattern of line seg-
            ments which connect pairs of points.  The file should con-
            tain two numbers per line.  The pair of numbers represents
            the row numbers of the two points that should be con-
            nected.

          filename.linecolors

            Line colors: a color for each line in the .lines file.
            The file should contain one color per line.  (It is best
            if the colors correspond to the colors used in brushing;
            see the later section on resources.)

          filename.nlinkable

            The number of rows to be linked for brushing and identifi-
            cation.  By default, nlinkable is equal to the number of
            rows in the data.  This feature can be used to link ordi-
            nary scatterplots with plots that have some decorations
            requiring additional points, such as clustering trees.

          filename.vgroups

            Variable groups: an integer for each column in the data.
            Each set of columns that is represented by the same inte-
            ger will grouped together for scaling and transformation.
            The file is just one long line of integers.  For example,
            an input file with four columns could have a .vgroups file
            containing the line 1 2 2 3.  The second and third columns
            are then grouped together.  The range of their plotting
            axes is be the same, and if column 2 is transformed, col-
            umn 3 is transformed at the same time.

          filename.rgroups

            Row groups: an integer for each row in the data.  Each set
            of rows that is represented by the same integer will
            grouped together for brushing.  In addition, line groups
            will be derived from the row groups:  all lines between
            points in the same row group will be in the same line
            group.  The file is just one column, and the numbers don't
            need to be in any sort of sequence.

          filename.missing

            A file identical in structure to filename.dat, where non-
            zero values indicate positions with missing (or censored,
            or otherwise exceptional) values.  This file represents
            the pattern of missing values in the data; it can be exam-
            ined in a separate XGobi window by selecting Launch
            missing data XGobi... from the Tools menu.

          filename.imp

            Multiple imputations of missing values: Each column should
            have a full set of imputed values.  The number of rows
            needs to be identical to the number of non-zero values in
            filename.missing, or the number of missing codes in
            filename.dat if filename.missing is not provided..  The
            imputed values should be given in their order in the data
            column by column.  For example, if filename.dat looks like
            this:

              10 NA 12 -3
              98  0 10  0
              77  3 NA -5
               1  2 NA 10
              NA NA  5 -8
               0  0 10 12

            (six cases, four variables, five missing values), then
            filename.imp with two sets of imputed values could look
            like this:

              54  37
               3   2
               4   1
              11  10
              13  11

            If the second column is selected for imputation (Select
            Impute missing values from the Tools menu), the full data
            matrix with imputations looks like this:

              10  2 12 -3
              98  0 10  0
              77  3 10 -5
               1  2 11 10
              37  1  5 -8
               0  0 10 12

          filename.resources

            Resources: a set of datafile-specific XGobi resources,
            which specify the size of the plotting window and some
            user-selection option settings.  The file is in the format
            of a standard X resource file.  It can be directly edited
            so that other resources can be specified.  See the later
            section on resource files for more information.

          All of the above files can be created outside of XGobi,
          using an editor or other UNIX utilities, and several of them
          (glyphs and colors, line segments and line color, resources)
          can be written out during an XGobi session, in which case
          they represent the results of interactions performed during
          that session.

     X11 RESOURCE FILES
          X11 resource files are used to control size, color, layout,
          labels, and various other windowing features.  The XGobi
          resources you are most likely to find useful set the sizes
          of the plotting window and the variable selection panel, the
          colors available for brushing, the font types and sizes, and
          the title appearing in the title bar of the X window.  Some
          examples follow:

          In this example, the first 5 of the 10 brushing colors are
          specified.  These colors should be drawn from the set of
          colors available on your workstation or X terminal, which
          you can probably determine using the X command 'showrgb.'

               *brushColor0: white
               *brushColor1: red
               *brushColor2: green
               *brushColor3: skyblue
               *brushColor4: yellow

          Here, the sizes of the plotting window and variable selec-
          tion panel are set.  All units are in pixels.  This file was
          created interactively during an XGobi session.

               *XGobi*PlotWindow.height: 120
               *XGobi*PlotWindow.width: 490
               *XGobi*VarPanel.width: 390

          These two resources allow the variable widgets to be reduced
          in size, which is helpful when there are many variables in
          the data.

               *XGobi*VarWindow.width: 36
               *XGobi*VarLabel.width:  36

          Here, the title and font have been adjusted for making a
          videotape.  An explanatory title and a large font are used.

               *XGobi.title:    XGobi: Experimental Laser Data
               *XGobi.iconName: XGobi: Laser
               *plotFont: -*-lucida-medium-r-normal-sans-20-*-*-*-*-*-*-*

          Several logical variables controlling XGobi's behavior can
          be defined in a resource file.  These are also represented
          by buttons, most of which are found on the Option menu
          accessed from the main panel.  Descriptions can be found in
          the help window for each button.

               *showAxes: True
               *showPoints: True
               *showLines: True
               *linkBrush: True
               *linkLineBrush: True
               *linkIdentify: True
               *linkTour: True
               *plotSquare: True
               *jumpBrush: True
               *reshapeBrush: True
               *carryVars: True
               *glyphType: 6
               *glyphSize: 1
               *defaultPrintCmd: lpr -Pps1

     AUTHORS
          Deborah Swayne (dfs@research.att.com)
          Dianne Cook (dicook@iastate.edu)
          Andreas Buja (andreas@research.att.com)

     CONTACT
          Deborah Swayne (dfs@research.att.com)

     SEE ALSO
          Sample data files are included in the XGobi distribution.

          For papers and further pointers, check the following web
          page:
          http://www.research.att.com/~andreas/xgobi/

          XGobi supports Remote Procedure Calls (RPCs) as a means for
          interprocess communication (IPC). For example, a link among
          XGobi, ArcView, and XploRe is currently being supported.
          For more details, see:
          http://www.galaxy.gmu.edu/~symanzik/AXX/


     BUGS
          Probably too numerous to mention, but you do the authors a
          favor if you report the ones you notice.








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