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]
[-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 largest distance, specify -std msd; to scale
using the median and largest distance, specify
-std mmd.
-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 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.