Table of Contents
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.
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:
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.
Block labels are associated with blocks drawn inside the circle. Blocks can be shaded or left empty.
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 Accelrys GCG (GCG) 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.
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 of what label file(s) ? @pgamma.fil
When your LaserWriter attached to tty07 is ready, press <Return>.
Here is the plot from the example session:
Here is another kind of plot generated using the file of file names pgamma2.fil:
This diagram schematically illustrates how information flows into and out of PlasmidMap.
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.
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.
MapSort run with the command-line parameter -PLAsmid can be used to generate a label file for PlasmidMap.
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.
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.
The input files for the example in Figure 1 are shown below. There are several format requirements:
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:)
(Circular) MAPSORT of: pgamma.seq check: 9889 from: 1 to: 5246
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 follow the ".." pattern. Blank lines and lines that start with an exclamation point (!) are ignored.
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,
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.
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
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
FromSymbol ToSymbol Output Appearance Comment
] ] ]----------------] Junction pointing with
[ [ ]----------------] Same as ]
| | |----------------| Bar
> > >----------------> Arrow pointing with
< < >----------------> Same as >
]H ]T [----------------[ Junction head and tail
>H > <----------------< Arrow head and tail
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
An example for PLASMIDMAP
Mismatch: 0 MinCuts = 1 MaxCuts: 2
With 149 enzymes: *
February 20, 1989
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
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
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.
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.
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.
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)
-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
-REMarks=3 sets the number of documentation lines below the circle
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
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.
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.
-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
You can set the parameters listed below from the command line.
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.
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.
Draws simple, straight major ticks. The default is to draw diamond-shaped major ticks. This is ignored if -NODRAWScale is selected.
Draws ranges with single lines instead of with multiple lines (the default), in the manner of -BOLDCircle.
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.
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.)
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.
Creates only one outer circle with no scale ticks. By default, there is a double outer circle containing major scale ticks.
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.
Suppresses the display of scale numbers on ticks outside the circle. Usually, these numbers outside the circle are displayed.
Sets PlasmidMap to draw dotted radial scaling lines from the outer circle toward the center.
Causes rays to be numbered with curved text when the -DRAWRays parameter is set.
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.
Selects a special shading style for the blocks. Usually, blocks are shaded with a cross-hatch pattern.
Causes PlasmidMap to prompt you interactively for each parameter value. By default, parameters are only taken from the command line and the initializing file.
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.
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.
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.
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.
Sets the height of the tick labels outside the circle.
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).
Specifies the height of the range labels.
Sets the height of the text inside the blocks. This parameter indirectly sets the width of the blocks.
Sets the height of the remarks below the circle. -REMarks=n must be selected to display remarks.
Sets the height of the title in the center of the circle. -TITle must be selected to display the title.
Sets the height of the scale numbers. -OUTERNumbers, -INNERNumbers, or both must be selected to display scale numbers.
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.
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.
Selects the color of the radial scale lines (and their numbers) inside the circle.
Selects the color of the scale ticks drawn between the double circle. This only makes sense if -DRAWScale is selected
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.
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.
Selects the color of the delimiters between the text labels outside the circle.
Selects the color of the title at the center of the circle and the remarks below the circle.
Selects the color of the circle.
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."
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.
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 GCG graphics programs. These and many others are described in detail in Section 5, Using Graphics of the User's Guide.
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.
Draws all text characters on the plot using Font 3 (see Appendix I).
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).
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).
Moves the plot to the right by 30 platen units (pan right).
Moves the plot up by 30 platen units (pan up).
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 13:59
Copyright (c) 1982-2005 Accelrys Inc. All rights reserved.
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