PLASMIDMAP(+)

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT/OUTPUT
RELATED PROGRAMS
RESTRICTIONS
SUGGESTIONS
INPUT FILES
GRAPHICS
<CTRL>C
ACKNOWLEDGEMENT
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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PlasmidMap draws a circular plot of a plasmid construct. It can display restriction patterns, inserts, and known genetic elements. The plot is suitable for publication, record keeping, or analysis. It is drawn from one or more labeling files such as those written by MapSort.

DESCRIPTION

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PlasmidMap has two purposes: 1) to display and store information about plasmid constructs; and 2) to publish or present information about such constructs.

PlasmidMap reads information about a plasmid from an input file and produces a labeled circular plot of that plasmid. The input file specifies the position of the labels and their styles -- tick, block, or range. An example of a suitable input file -- in this case containing restriction site information -- is the output file from a MapSort session run with the command-line parameter -PLAsmid. PlasmidMap can accept more than one labeling file as input, plotting the information from each file on the same circular map. You can specify more than one file by using a name containing wildcard characters or by using a file of file names (a text file you create that starts with a line containing two dots (..) and has one file name per line thereafter). PlasmidMap simply transfers information from these labeling files to graph paper; it does not map the sequence by itself.

PlasmidMap can draw three kinds of labels:

Ticks

Tick labels are associated with a single base and are printed next to a tick around the outside of the circle. Tick labels have been used historically to identify restriction sites and coordinates.

Blocks

Block labels are associated with blocks drawn inside the circle. Blocks can be shaded or left empty.

Ranges

Range labels are associated with lines drawn inside the circle. Ranges can start and end with arrow heads, arrow tails, blunt ends, junction heads, and junction tails. The arc for a range can be narrow or bold.

Every label is defined by a name, a starting coordinate, an ending coordinate, a strand, a color, and a style (tick, block, or range). A range must also include a beginning and ending character to indicate the type of head and tail to draw. The format of the input file is described in detail below.

You can set over 30 different parameters for PlasmidMap. Therefore, the values of the parameters are normally defined in an initializing file rather than by a series of interactive prompts. All parameters have default values, so only parameters that you wish to change need to be specified in the initializing file.

As with all Wisconsin Package(TM) programs, you can override the values set in the initializing file by using command-line parameters. Values set on the command line take precedence over values in the initializing file.

EXAMPLE

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In this example, the input file to PlasmidMap is a file of file names that names two labeling files: 1) a file with tick information written by MapSort; and 2) a file with range information that was entered by hand.


% plasmidmap

  PLASMIDMAP of what label file(s) ?  @pgamma.fil

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

%

OUTPUT

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Here is the plot from the example session:

Figure 1

Here is another kind of plot generated using the file of file names pgamma2.fil:

Figure 2

INPUT/OUTPUT

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This diagram schematically illustrates how information flows into and out of PlasmidMap.

Input

You can map a sequence and save the restriction cut positions in a tick file with MapSort (-PLAsmid). The resulting tick file can be displayed without any modification by PlasmidMap.

You can manually create another file with range and block information and specify both this file and the tick file to PlasmidMap. (PlasmidMap displays all of the files you specify on the same circular graph.) The input file specification to PlasmidMap can be either a multiple file specification such as pgamma.t* or a file of file names, such as @pgamma.fil.

You can use the Fetch program to obtain a copy of the file plasmidmap.init that you can edit to change any of the general attributes of the graph.

Output

You can display the graph on any graphics device each time you run PlasmidMap. When you have the picture you want, you can save the plot as a figure file (suitable for input to the Figure program) by including -FIGure on the command line. The resulting figure file (called plasmidmap.figure) can be customized further and stored for display at a later time on any device.

The Figure program, with the -PSINClude parameter, can also make a file of PostScript instructions for inclusion in a Red document.

RELATED PROGRAMS

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MapSort run with the command-line parameter -PLAsmid can be used to generate a label file for PlasmidMap.

RESTRICTIONS

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The displays become very crowded if many labels are plotted. Most raster devices (CRT screens and dot matrix printers) do not have enough resolution to plot very small characters or text along a curve, so the final product of PlasmidMap should be drawn on a high quality plotter such as the Hewlett Packard 7475 or 7550.

SUGGESTIONS

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Several plots can be drawn on the same page by changing the -LOCAtion variable. The radius and text sizes are scaled down appropriately so that only the -LOCAtion value needs to be changed.

You can make concentric restriction maps by running MapSort with the command-line parameter -FRAGments and using the output for PlasmidMap with -NOSORTBlocks -SHADEDensity=0 on the command line. Figure 2 is an example of what this output would look like.

INPUT FILES

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The input files for the example in Figure 1 are shown below. There are several format requirements:

First Line

The first non-blank line of the first label file in the set of label files that you specify must define the following information:
1) the name of the molecule (a string following the word of:)
2) the checksum of the molecule (any integer following the word check:)
3) the beginning of the molecule (an integer following the word from:)
4) the end of the molecule (an integer following the word to:)

Example:


(Circular) MAPSORT of: pgamma.seq check: 9889 from: 1 to: 5246

Text Header

Any amount of text may follow the first line until a line contains the ".." pattern. Some of this text may be included in the plot by using the -REMarks command-line parameter, described below.

Label Data

Label data follow the ".." pattern. Blank lines and lines that start with an exclamation point (!) are ignored.

Every label has eight attributes that describe how the label will look. The attributes must be separated by spaces. The eight attributes or fields that make up a label record are: Name, FromCoordinate, ToCoordinate, Strand, Color, FromSymbol, ToSymbol, and Style. If a record does not have something in all eight fields, the label is not drawn.

Name

The name is the text that appears next to the tick or range or within the block. The name must be typed as a contiguous string of characters. Since attributes are separated by spaces, you cannot type any space characters within the name. If you want a space to appear within the name on the plot, type an underscore character (_) in the name where you want the space to appear. PlasmidMap substitutes a space for the underscore character when it makes the label. If the only character in the Name field is an underscore character, there is no visible label in the output.

From and To

The from: coordinate is the beginning of a range or block or the position of a tick. The to: coordinate is the end of a range or block. The from: and to: coordinates are taken in an counterclockwise sense if the reverse strand is specified (a minus sign appears in the Strand field); otherwise, they are clockwise. The to: coordinate is ignored for tick labels but must be included nevertheless. If the coordinates are not both within the length of the molecule, or if both cannot be interpreted, the label is not drawn and you are notified.

Strand

Strand defines which way ranges and blocks are defined. When a minus sign (-) appears in the Strand field, ranges are counterclockwise (anti-clockwise). When a plus sign (+) appears, ranges are clockwise. A period (.) in this field can be used to imply that the strand is irrelevant, as in the case of ticks. For ranges and blocks, any character other than the minus sign is treated as a plus sign (clockwise).

Color

Color specifies the color of the label and its associated tick, range, or block. The colors can be numbers from 1 to 32 or the names of the four standard colors: black, green, blue, and red. If you specify a number greater than the number of colors supported on your graphics device, a supported color is substituted. If the color field cannot be interpreted, the label is the default color for that label type. See the paragraphs below about -TICKColor and -RANGEColor. Block labels default to black.

FromSymbol and ToSymbol

These are characters that affect the appearance of the ends of ranges. They are ignored for blocks and ticks. Normally, arrows and junctions point in the same direction as the from: and to: coordinates. That is, they make arrows that point in the direction defined by Strand. You can make other end characters by explicitly defining the type of arrow or junction you want by adding H for head or T for tail. The supported end characters are represented in the table below. If an end symbol cannot be interpreted, a vertical bar (|) is drawn.


FromSymbol ToSymbol Output Appearance       Comment
]          ]        ]----------------]  Junction pointing with Strand
[          [        ]----------------]  Same as ]
|          |        |----------------|  Bar
>          >        >---------------->  Arrow pointing with Strand
<          <        >---------------->  Same as >
]H         ]T       [----------------[  Junction head and tail
>H         >        <----------------<  Arrow    head and tail

Style

Style can have one of three values: tick, range, or block. If the Style field cannot be interpreted as one of these three, the label is not drawn.

Here is some of the tick label file (pgamma.tick) used for the example session for Figure 1; Figure 2 used the file pgamma.block:


 (Circular) MAPSORT of: pgamma.seq  check: 9889  from: 1  to: 5246
_
Figure 1
An example for PLASMIDMAP

 Mismatch: 0  MinCuts = 1  MaxCuts: 2
 With 149 enzymes: *

                         February 20, 1989  13:47

     Name     From       To   Strand  Color  FromSymbol  ToSymbol  Style ..

AatII         4292     4292      .     Blue       .          .     Tick
AflIII        2477     2477      .    Green       .          .     Tick
AlwNI         2893     2893      .     Blue       .          .     Tick

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

XcaI          2250     2250      .    Black       .          .     Tick
XhoI          5093     5093      .    Green       .          .     Tick
XmaIII         941      941      .    Green       .          .     Tick

Here is the range label file (pgamma.ranges) used for the example session for Figure 1; Figure 2 used the file pgamma2.ranges:


Ranges for pgamma.seq:

assembled From EMBL:pbr322

locus       pbr322       4363 bp    dna   circular  updated   02/22/85
definition  plasmid pbr322, complete genome.

and from GenDocData:gamma.seq

Name     From       To   Strand  Color FromSymbol ToSymbol Style ..

! the genes from pbr322

Tet_Resistance      86  1276  +  Black     <      <        Range
Beta_Lactamase    3298  4086  -  Black     <      <        Range

! human fetal beta globin a gamma coding regions

CAP_Site         4566   4566  .  Black     .      .        Tick
___              4618   4709  .  Black     |      |        Range
A_Gamma          4832   5054  .  Black     |      |        Range

! blocks for vector and insert

pBR322_cut_at_RI    1   4363  +  Blue      ]      ]        Range
Insert           4364   5246  +  Blue      |      |        Block

GRAPHICS

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The Wisconsin Package 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 the Wisconsin Package supports. See Chapter 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.

ACKNOWLEDGEMENT

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PlasmidMap was inspired by the PLASMAP program written at Eli Lilly and Company by Barry Stone (Stone et al., Nucl. Acids Res. 12(1); 465-472 (1984)). The Wisconsin Package program was written by William Martin and Philip Delaquess working at the University of Wisconsin with funds provided by the Monsanto Company. We are very grateful to Dr. Peter Olins of Monsanto who gave us many of the best ideas for PlasmidMap.

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. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % plasmidmap [-INfile1=]@pgamma.fil -Default

Prompted Parameters: None

Local Data Files:

-INITialize=plasmidmap.init    sets the optional parameters for PlasmidMap
                                 (default file is in GenRunData directory)

Optional Parameters:

-NOBOLDCircle         draws a thin circle with a single line
-NOBOLDMajorticks     draws simple, straight major ticks (instead of the
                        default diamond-shaped ones)
-NOBOLDRanges         draws thin ranges with single lines
-SORTRanges           places smaller ranges toward the outside of the circle
-NOSORTBlocks         places blocks from the outside inward in the order
                        they are found in the label file
-NOCAPtion            suppresses the plot caption to the left of the plot
-NODRAWScale          creates only one outer circle with no scale ticks
-NOARCText            suppresses curved text (range labels and inner numbers)
-NOOUTERNumbers       suppresses displaying scale numbers on ticks
                        outside the circle
-DRAWRays             draws dotted radial scaling lines from the outer
                        circle toward the center
  -INNERNumbers         numbers the radial scaling lines
-TITle[="MyName"]     titles the plot
-HALFShade            selects a non-crosshatched shading pattern for blocks
-PROmpts              prompts interactively for each optional parameter
-SHADEDensity=3       selects the density for shading within blocks
                        (0=none, 1=sparse, 2=medium, 3=dense (default), 4=solid)
LOCAtion=1            sets the position of the plot on the page
                        (1=center, 2=left-center, 3=right-center, 4=upper-left,
                         5=lower-left, 6=upper-right, 7=lower-right)
-ORIGin=1             selects how to number the origin of the molecule
                        (0=display the beginning coordinate, 1=display the
                         ending coordinate, 2=display both begin and end)
-EMPHasis=0           selects the emphasis of the origin on the plot
                        (0=no emphasis, 1=boldface, 2=parentheses, 3=asterisks)
-MMTHeight=5.33       sets the height of tick labels outside the circle
-MINTHeight=3.2       sets the minimum height of tick labels
-MMRHeight=3.7        sets the height of the range labels
-MMBHeight=4.0        sets the height of text inside blocks
-MMREMARKHeight=6.0   sets the height of the remarks below the circle
-MMTITLEHeight=10.0   sets the height of the title in the center of the circle
-MMNUMBERHeight=3.5   sets the height of the scale numbers
-MMSCALETLength=3.3   sets the length of small ticks inside the double circle
-TICKColor=1          sets the default color of tick labels
-RAYColor=4           sets the color of radial scale lines and their numbers
-SCALEColor=4         sets the color of small ticks inside the double circle
-RANGEColor=1         sets the default color of the ranges
-NUMBERColor=4        sets the color of the scale numbers outside the circle
-DELIMColor=4         sets the color of delimiters between coincident
                        text labels outside the circle
-TITLEColor=1         sets the color for the center title and for the
                        remarks below the circle
-CIRCLEColor=1        sets the color of the circle
-SEParator1="/"       sets the delimiter between coincident tick labels
-SEParator2="<"       sets the delimiter between coalesced labels with
                        different locations
-REMarks=3            sets the number of documentation lines below the circle

All GCG graphics programs accept these and other switches. See the Using
Graphics chapter 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 Chapter 4, Using Data Files in the User's Guide.

The file plasmidmap.init in the genrundata directory or in your working directory is used to initialize the command line. Anything that you type on the command line takes precedence over settings in the file. Here is the public version of the initializing file:


MAPPLASMID command line initializing file.

5/05/86 ..

! Switches:

-BOLDCircle       ! draws a thick circle

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

! Optional shading of "blocks"

-SHADEDensity=3   ! 0=noshading, 1=sparse, 2=medium, 3=dense, 4=solid

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

! Character heights (in millimeters for location 1 on 11 x 17 paper):

-MMTHeight=5.33   ! height of tick labels

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

! GCG colors are numbered 1=Black, 2=Green, 3=Blue and 4=Red.

-TICKColor=1      ! color of the ticks outside the circle

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

For Figure 2, the following parameters were used on the command line to override plasmidmap.init settings:

% plasmidmap -NOSORTBlocks -SHADEDensity=0

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

While PlasmidMap is designed to be controlled with a command-line initializing file, all of its features can be defined on the command line. If a parameter is defined both on the command line and in the initializing file, the value on the command line is used. If a parameter is not set, either on the command line or in the initializing file, then PlasmidMap uses a default value.

-NOBOLDCircle

draws the circle with a single line. The default is to draw a bold outer circle. A bold circle is drawn with several closely spaced lines.

-NOBOLDMajorticks

draws simple, straight major ticks. The default is to draw diamond-shaped major ticks. This is ignored if -NODRAWScale is selected.

-NOBOLDRanges

draws ranges with single lines instead of with multiple lines (the default), in the manner of -BOLDCircle.

-SORTRanges

allows you to sort the ranges, putting smaller ranges toward the outside of the circle. This may make more efficient use of space. The default is to place ranges from the outside inward in the order in which they occur in the label file. This gives you control over range placement.

-NOSORTBlocks

places blocks from the outside inward in the order in which they occur in the label file, instead of sorting them. The default is to sort the blocks by size. (See the paragraph above about range sorting.)

-NOCAPtion

suppresses the standard GCG plot caption to the left of the plot. By default, the first line of the first label file is shown along with your name and the date.

-NODRAWScale

creates only one outer circle with no scale ticks. By default, there is a double outer circle containing major scale ticks.

-NOARCText

suppresses curved text (range labels and inner numbers). Curved text suppression may be necessary for CRT screens and raster devices that cannot successfully display characters on a slant. By default curved text is displayed.

-NOOUTERNumbers

suppresses the display of scale numbers on ticks outside the circle. Usually, these numbers outside the circle are displayed.

-DRAWRays

sets PlasmidMap to draw dotted radial scaling lines from the outer circle toward the center.

-INNERNumbers

causes rays to be numbered with curved text when the -DRAWRays parameter is set.

-TITle="MyName"

designates the title for the plot, which is displayed in the middle of the circle. By default, PlasmidMap uses the sequence name and length. If you specify -NOTITle, PlasmidMap puts a small dot in the middle of the plot to help you find the positions along each concentric ring that have the same coordinate.

-HALFShade

selects a special shading style for the blocks. Usually, blocks are shaded with a cross-hatch pattern.

-PROmpts

causes PlasmidMap to prompt you interactively for each parameter value. By default, parameters are only taken from the command line and the initializing file.

-SHADEDensity=3

selects the density of the shading inside the blocks: 0 selects no shading, 1=sparse, 2=medium, 3=dense (the default), and 4=solid. Shading is accomplished with a cross-hatch pattern unless -HALFSHADE is selected.

-LOCAtion=1

defines the position of the plot on the page: 1 (the default) makes a full-size plot in the center of the paper; 2 and 3 make half-size plots to the left and right of center; and 4, 5, 6, and 7 make quarter-size plots in the northwest, southwest, northeast and southeast corners.

-ORIGin=1

selects the way the molecule's origin (beginning coordinate) is displayed: 0 means display the beginning coordinate minus one; 1 (the default) means display the ending coordinate of the molecule; and 2 means display both the beginning minus one and the ending coordinates of the molecule.

-EMPHasis=0

allows the origin to be emphasized in any of several different ways: 0 gives no emphasis, 1=boldface, 2=parentheses, and 3=asterisks.

The next six parameters set character heights. The heights are in millimeters when you plot with -LOCAtion=1 on a page that is 11 x 17 inches. If all the labels won't fit given the size you have specified, the size may be reduced automatically.

-MMTHeight=5.33

sets the height of the tick labels outside the circle.

-MINTHeight=3.2

sets the minimum height of the tick labels. PlasmidMap first attempts to use the value set by -MMTHeight. If ticks are too crowded to be written with that height, then the height is reduced automatically. However, if this height must be made less then your selected -MINTHeight, then adjacent tick labels are coalesced into single ticks. That is, a tick in the final plot may actually be the average location of more than one label in the input file. This parameter allows you to trade resolution (small minimum) for readability (large minimum).

-MMRHeight=3.7

specifies the height of the range labels.

-MMBHeight=4.0

sets the height of the text inside the blocks. This parameter indirectly sets the width of the blocks.

-MMREMARKHeight=6.0

sets the height of the remarks below the circle. -REMarks=n must be selected to display remarks.

-MMTITLEHeight=10.0

sets the height of the title in the center of the circle. -TITle must be selected to display the title.

-MMNUMBERHeight=3.5

sets the height of the scale numbers. -OUTERNumbers, -INNERNumbers, or both must be selected to display scale numbers.

-MMSCALETLength=3.3

sets the length of the small ticks inside the double circle when -DRAWScale is selected.

The next eight parameters define colors with numbers. For all features, 1=black, 2=green, 3=blue, and 4=red. Numbers up to 32 can be used if your graphics device supports additional colors.

-TICKColor=1

selects the default color of tick labels. If a color is given in the input file, then that color is used instead. Each tick on the outside of the circle is drawn with the same color as the first label it points to.

-RAYColor=4

selects the color of the radial scale lines (and their numbers) inside the circle.

-SCALEColor=4

selects the color of the scale ticks drawn between the double circle. This only makes sense if -DRAWScale is selected

-RANGEColor=1

selects the default color of the ranges. If a color is given in the input file, then that color is used instead. Ranges are always drawn with the same color as their corresponding text.

-NUMBERColor=4

selects the color of the text for the scale numbers outside of the circle. To plot outer scale numbers in the first place, -OUTERNumbers must be selected.

-DELIMColor=4

selects the color of the delimiters between the text labels outside the circle.

-TITLEColor=1

selects the color of the title at the center of the circle and the remarks below the circle.

-CIRCLEColor=1

selects the color of the circle.

-SEParator1="/"

selects the delimiter between tick labels having the same location. If, for example, AhaII and NarI both cut at base 551, the plot contains a single tick at 551 with the label "AhaII / NarI."

-SEParator2="<"

selects the delimiter between tick labels having different, nearby locations. If AhaII cuts at 551, and BanI cuts at 550, and their surroundings are so crowded that they must be coalesced, then the plot contains a single tick with the label BanI < AhaII. Compare this situation with the equal-base situation described above. Also see the paragraph about -MINTHeight for information on coalescing overly crowded ticks.

-REMarks=3

controls the number of lines of documentary header to center below the circle. All of the non-blank text lines in the first label file, excluding the first line and up to but not including the line containing "..", are available for inclusion in the plot. The more lines included, the smaller they are; ten lines are allowed, but readability is greatly diminished. Use -REMarks=0 to suppress documentation. Documentary lines are centered after having leading and trailing blanks removed, and multiple blanks between words are reduced to single blanks. You may use underscore characters to force additional blanks.

The parameters below apply to all Wisconsin Package graphics programs. These and many others are described in detail in Chapter 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: December 9, 1998 16:27 (1162)

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