Delila Program: dnaplot

dnaplot program

Documentation for the dnaplot program is below, with links to related programs in the "see also" section.

{   version = 3.47; (* of dnaplot.p 2005 May 23}

(* begin module describe.dnaplot *)
(*
name
   dnaplot: plot Ri values for one or more large DNA sequences

synopsis
   dnaplot(dnain: in, dnaout: out, dnaplotp: in,
           positions: in, dnasymbols: in, output: out)

files
   dnain:  A data input file created by scan.  It contains header lines that
       begin with asterisks ('*') that are copied to dnaout.  Remaining lines
       are the data in columns, ending with end of file.

   dnaout: output in PostScript format

   dnaplotp: Parameter file for dnaplot, which is configured as followed:

       frompos topos         These two integers are the positions on the
                             sequence which the graph will represent.  If,
                             instead, the first character on the line is 'r',
                             then these numbers are read from the positions
                             file for each sequence.

       sCol pCol cCol vCol   columns numbers for reading from the dnain file:
                             sCol = piece number
                             pCol = column number of piece name
                             cCol = piece coordinate
                             vCol = value (Ri evaluation)

       numperpg              number of graphs per page
       numperln              number of base pairs per line
       bitlower bitupper     lower and upper bounds of bits to display

       orix oriy             x, y origin of plot (in cm)
       xaxlength yaxlength   length of the x and y axes in cm
       showaxis              t=true means show coordinate axis to dnaout
       xinterval yinterval   size of intervals on axes to plot
       xsubint   ysubint     x and y sub intervals to mark
       xwidth    ywidth      width of numbers in characters
       xdecimal  ydecimal    number of decimal places
       xticlength xticdx xticdy  length of tic mark and shift of number (cm)
       yticlength yticdx yticdy  length of tic mark and shift of number (cm)
       sequencelabel         t=true means print sequence number on graphs
       xaxislabel            the label for the x axis
       yaxislabel            the label for the y axis
       plottype              How to draw the plot:
                             z = lines from zero to value
                             b = lines from bottom of graph to value
       dodash                Whether to put vertical dashed lines around
                             segments of continuous sequence.  This is
                             important for distinguishing between the absence
                             of sequence and low Ri values, but this often gets
                             in the way, so it can be turned off:
                             d = do dashes
                             n = no dashes
       thelinewidth          The width of the plot lines in bases.

   positions:  If the first character on the first line of the parameter file
      is an 'r' then this file will be read to determine the positions to graph
      for each sequence.  The file consists of pairs of integers, one pair per
      line, representing the first (frompos) and last (topos) coordinates to be
      plotted.

   dnasymbols: If the file is not empty, then it contains information on how
      and where to plot special symbols to make marks on the graph.  Each line
      has 5 values:
         symbol (first character): the type of symbol to draw:
            c = circle
            s = square
            t = triangle
         symboltype (second character): the way to draw the symbol:
            s = stroked as a solid line
            f = filled
            d = dotted line
         symbolplacement (third character): where to put the symbol on the graph:
            a = use absolute location (given by symbolbits) on graph
            r = use relative location (given by symbolbits) from current Ri value
         symbolbits (real): the distance in bits
         symbolsize (real): diameter of a circle or side of square and triangle
            relative to the spacing between graph lines.  A value of 1 fits
            between the lines.
         piece number (integer):  The number of the fragment to mark,
            as given in the dnain file
         piece coordinate (integer):  the coordinate on the piece to mark
            as given in the dnain file

        ********************************************************************
        * The symbols MUST be in increasing order of position in the plot! *
        ********************************************************************

        Lines that are empty or begin with "*" are ignored.

   output: messages to the user

description
   dnaplot creates a PostScript graph of information content (or
   other values) versus position on a DNA sequence.

examples

dnasymbols
The line:
csa 15 0.5 1 100
means place a circle, stroked, at absolute 15 bits, 0.5 size,
for sequence 1 at coordinate 100.

documentation

see also
   scan.p, xyplo.p, dbbk.p

author
   Stacy L. Bartram, modified by Tom Schneider

bugs

   The program cannot handle negatively numbered base systems because the axis
   cannot give decreasing numbers (yet or ever).  These simply come out as
   blank (or the program will halt, depending on the version).

technical notes

*)
(* end module describe.dnaplot *)
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