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Name

xgobi - interactive dynamic graphics program for data visualization

Synopsis

xgobi [ X options ] [ -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:

Cycling rapidly through two-variable scatter plots.

Three-dimensional rotation, including trackball control.

Grand tour rotation: a smooth randomized sequence of two-dimensional projections in order to explore a higher-dimensional point cloud.

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

Scaling: moving and reshaping the plot interactively.

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

Linking: Brushing, identification and touring are linked; that is, actions in the window of one XGobi process are immediately reflected in another XGobi window displaying the same data.

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

Transformation: A menu of data transformations is available.

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

Online help: Most of the XGobi buttons and windows have associated help files that can be displayed during an XGobi session. Click on the Help 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 S (1) . Execute help(xgobi) within S for information.

Options

-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 contained within the plotting window, using the argument -dev x, where x is a real number between 0 and 100. The default is 2.

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; rows must be distinguished by carriage returns, and columns can be separated by any amount of white space. (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.rowfilename.rowlabfilename.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.colfilename.collabfilename.columnfilename.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, representing a row or case of the data. The file should contain one color per line. (It is probably best if the colors 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 segments which connect pairs of points. The file should contain two numbers per line. The pair of numbers represents the row numbers of the two points that should be connected.

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 identification. By default, nlinkable is equal to the number of rows in the data. This feature can be used to link ordinary 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 integer 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 and third columns are then grouped. The range of their plotting axes is be the same, and if column 2 is transformed, column 3 is transformed at the same time.

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 stored 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 selection 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

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 and in the full-length user’s manual.


*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@bellcore.com), Dianne Cook (dcook@iastate.edu), and Andreas Buja (andreas@bellcore.com)

Contact

Deborah Swayne (dfs@bellcore.com)

See Also

Sample data files are included in the XGobi distribution.

Deborah Swayne, Dianne Cook and Andreas Buja (1991), User’s Manual for XGobi, a Dynamic Graphics Program for Data Analysis Implemented in the X Window System (Version 2), Bellcore Technical Memorandum.

Bugs

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


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