STATPLOT

Table of Contents

FUNCTION

DESCRIPTION

EXAMPLE

FUNCTION

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StatPlot plots a set of parallel curves from a table of numbers like the table written by the Window program. The statistics in each column of the table are associated with a position in the analyzed sequence.

DESCRIPTION

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StatPlot is a display program for programs like Window that make sliding window measurements on a sequence. The statistics in each column of the table are associated with some position in a sequence. StatPlot figures out a scale for each column and then plots all of the statistics in parallel. You can choose the density in bases per cm along the horizontal axis so that different runs of StatPlot may be compared.

EXAMPLE

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Here is a session using StatPlot to plot the functions from the example session with Window:

% statplot

  STATPLOT what stat file ?  gamma.wdw

  gamma.wdw contains 6 columns of 134 statistics for:

             Name   Check   Begin     End       Dir

        gamma.seq    6474       1     500   forward

  The minimum density for a one-page plot is 23.15 bases/cm.

  What density would you like (* 23.15 *) ?

  STATPLOT will take 1 pages.  Would you like to:

       P)lot the statistics

       D)ifferent density

       G)et another stat file to plot

       Q)uit

  Please select one (* P *):

  When your LaserWriter attached to tty07 is ready, press <Return>.

       P)lot the statistics

       D)ifferent density

       G)et another stat file to plot

       Q)uit

 Please select one (* P *):  Q

OUTPUT

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The plot from this session is shown at the end of this program entry.

INPUT FILES

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The output files from some GCG programs, such as Window, can be read as input by StatPlot. You could also create an input file using a text editor. If you do so, here are the format requirements for the input file to StatPlot.

The first line of the file must identify the sequence, checksum, and range after the words of:, check:, from:, and to:. The word reverse identifies reversed sequence ranges. Reversed ranges are numbered backwards on GCG plots.

The second non-blank line is printed on the plot without interpretation.

The dividing line (the line containing the "..") is read and the words from the second column onwards are taken to be the column headings for labeling each part of the plot. The number of words in this line between the first word (in this example, "position") and the ".." is taken to be the number of columns of statistics to be plotted. There must be a space between the last column heading and the two periods.

The data start two lines below the dividing line. The numbers are in the format I8, 6F12.3. This means that the position numbers are integers right justified in the first eight character columns. Each statistic has three figures to the right of the decimal and is right justified in a field 12 character-columns wide.

Here is some of the input file gamma.wdw, which you can Fetch for further inspection:

 WINDOW of: gamma.seq  check: 6474  from: 1  to: 500

 Window: 100  Shift: 3  MatchType: Subset MisMatch: 0

Human fetal beta globins G and A gamma

from Shen, Slightom and Smithies,  Cell 26; 191-203.

Analyzed by Smithies et al. Cell 26; 345-353.

                         October 13, 1998 13:06

Position C(obsrv) G(obsrv) CG(obsrv) CG_ob-ex(l) GC(obsrv) GC_ob-ex(l)  ..

      50   17.000   30.000     1.000      -4.049     4.000      -1.049

      53   19.000   29.000     1.000      -4.455     5.000      -0.455

      56   17.000   30.000     1.000      -4.049     5.000      -0.049

     /////////////////////////////////////////////////////////////////

     443   31.000   14.000     0.000      -4.297     2.000      -2.297

     446   32.000   14.000     0.000      -4.435     2.000      -2.435

     449   32.000   13.000     0.000      -4.118     2.000      -2.118

RELATED PROGRAMS

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Window makes a table of the frequencies of different sequence patterns within a window as it is moved along a sequence. A pattern is any short sequence like GC or R or ATG. You can plot the output with the program StatPlot.

RESTRICTIONS

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No more than six columns of measurements are allowed. No more than 300,000 measurements may appear in each column. There are a number of input file format restrictions discussed above under the INPUT FILES topic.

On Hewlett Packard plotters, density in bases per centimeter is only defined for paper that is 11 x 17 inches.

GRAPHICS

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Accelrys GCG (GCG) must be configured for graphics before you run any program with graphics output! If the%setplot command is available in your installation, this is the easiest way to establish your graphics configuration, but you can also use commands like % postscript that correspond to the graphics languages GCG supports. See Section 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.

<CTRL>C

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If you need to stop this program, use <Ctrl>C to reset your terminal and session as gracefully as possible. Searches and comparisons write out the results from the part of the search that is complete when you use <Ctrl>C. The graphics device should stop plotting the current page and start plotting the next page. If the current page is the last page, plotters should put the pen away and graphic terminals should return to interactive mode.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional.

STATPLOT does not support complete command-line control.

Local Data Files:

-MARk=gamma.mrk   marks the plot with known features

Optional Parameters:

-LABel            makes vertical axis labels on every page

-POInt            makes points instead of a continuous curve

-CONsistent       scales every field the same

-SCAling          lets you set each fields scale limits interactively

All GCG graphics programs accept these and other switches. See the Using

Graphics section of the USERS GUIDE for descriptions.

-FIGure[=filename]  stores plot in a file for later input to FIGURE

-FONT=3             draws all text on the plot using font 3

-COLor=1            draws entire plot with pen in stall 1

-SCAle=1.2          enlarges the plot by 20 percent (zoom in)

-XPAN=10.0          moves plot to the right 10 platen units (pan right)

-YPAN=10.0          moves plot up 10 platen units (pan up)

-PORtrait           rotates plot 90 degrees

LOCAL DATA FILES

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The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Section 4, Using Data Files in the User's Guide.

If you are studying a sequence with known features, this program can mark the plot with small boxes showing the positions of these features. The presence of a file in your directory with the same name as your sequence and the filename extension .mrk causes the program to mark each range specified in the file. You can provide a marking file on the command line with an expression like -MARk=gamma.mrk. The file gamma.mrk contains information about the format of marking files. The figure for the example session shows marked regions.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line.

-LABel

Makes vertical axis labels on both vertical axes of every page of a multi-page plot.

-POInt

Places a point at each measurement instead of drawing a continuous curve.

-CONsistent

Because StatPlot scales each field to use the whole physical vertical axis dimension, it may cause vertical exaggeration when you want to compare similar measurements. You can use the -CONsistent parameter to cause StatPlot to plot all of the measures with the same scaling. This scaling may cause weird-looking results if the measures are of different kinds as in the plot in the example. The -SCAling parameter allows you to choose the absolute scaling for each field.

-SCAling

Allows you to set the scaling on the vertical axis. If you use this parameter you are asked for the bottom and top of each panel in the plot. The query shows the defaults calculated for each panel.

-MARk=gamma.mrk

If you are studying a sequence with known features, this program can mark the plot with small boxes showing the positions of these features. The presence of a file in your directory with the same name as your sequence and the file name extension .mrk causes the program to mark each range specified in the file. The file gamma.mrk contains information about the format of marking files.

The parameters below apply to all GCG graphics programs. These and many others are described in detail in Section 5, Using Graphics of the User's Guide.

-FIGure=programname.figure

Writes the plot as a text file of plotting instructions suitable for input to the Figure program instead of sending it to the device specified in your graphics configuration.

-FONT=3

Draws all text characters on the plot using Font 3 (see Appendix I).

-COLor=1

Draws the entire plot with the pen in stall 1.

The parameters below let you expand or reduce the plot (zoom), move it in either direction (pan), or rotate it 90 degrees (rotate).

-SCAle=1.2

Expands the plot by 20 percent by resetting the scaling factor (normally 1.0) to 1.2 (zoom in). You can expand the axes independently with -XSCAle and -YSCAle. Numbers less than 1.0 contract the plot (zoom out).

-XPAN=30.0

Moves the plot to the right by 30 platen units (pan right).

-YPAN=30.0

Moves the plot up by 30 platen units (pan up).

-PORtrait

Rotates the plot 90 degrees. Usually, plots are displayed with the horizontal axis longer than the vertical (landscape). Note that plots are reduced or enlarged, depending on the platen size, to fill the page.

Printed: May 27, 2005 14:46

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