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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