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{ 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 *) {This manual page was created by makman 1.44}

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