man page for xgobi
xgobi man page

NAME
xgobi - interactive dynamic graphics program for data visualization

SYNOPSIS
xgobi [ X options ] [-mono] [-subset n] [-only n/N] [-only a,n] [-std mmx|msd|mmd] [-dev std_deviation] [-version] [-scatmat] 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:

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 sample size and sampling method during the session. -only n/N Specify the size n of the random sample of the data to be read in on startup from a file of N rows. In constrast to subset, this option does not read in all data. -only a,n Specify the initial row a and the number of rows n in the consecutive block of data to read in. In constrast to subset, this option does not read in all data.

-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.

-mono
Emulate a black-and-white display. This simplifies producing pictures for many publications.

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

-scatmat
Build a scatterplot matrix of the input data, and display it in the plotting window. It is linked by default to other xgobi windows.

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.

To add a short label to be used in the parallel coordinates plot, use the vertical bar "|" as a field separator and add the short name, so each line looks like this: fullname|shortname.

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 .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, column 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 examined 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 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

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)

SEE ALSO
For papers, sample data files, and further pointers, check the following web page: http://www.research.att.com/areas/stat/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.