grphwarpi: Creates graphics for genewarpi-generated time alignments (interpolative time warping). program version = 1.0 (20000814-10:43:38) Supported parameters: -Padfeature (between features padding size) On time series and alignment diagrams, fraction of space allotted to each feature (gene) time series that is used to provide padding between adjacent feature graphs. syntax: -Padfeature pos-number; Not required; Default = .1. -Padleft (left padding size) Fraction of graphic width used for left padding. "Padding" is extreme border space that is not written into. syntax: -Padleft non-neg-number; Not required; Default = .08. -Padlower (lower padding size) Fraction of graphic height used for lower padding. "Padding" is extreme border space that is not written into. syntax: -Padlower non-neg-number; Not required; Default = .08. -Padright (right padding size) Fraction of graphic width used for right padding. "Padding" is extreme border space that is not written into. syntax: -Padright non-neg-number; Not required; Default = .05. -Padupper (upper padding size) Fraction of graphic height used for upper padding. "Padding" is extreme border space that is not written into. syntax: -Padupper non-neg-number; Not required; Default = .02. -bordleft (left border size) Fraction of graphic width to the left of the graph used for left border. The left border contains y axis labels, the y axis title and feature (gene) labels. syntax: -bordleft pos-number; Not required; Default = .2. -bordlower (lower border size) Fraction of graphic height below the x axis of the graph used for lower border. The lower border contains x axis labels and the graphic title. syntax: -bordlower pos-number; Not required; Default = .09. -breakdownleft (left border breakdown) Four fractions that determine size of feature labels, padding, size of y axis labels, and more padding, in the left border. Must add up to 1.0. syntax: -breakdownleft pos-number pos-number-1 pos-number-2 pos-number-3 pos-number-4; Not required; Default = .55 .05 .30 .10. -breakdownlower (lower border breakdown) Three fractions that determine where in lower border the x axis labels, graph title, and additional information line occur. syntax: -breakdownlower pos-number pos-number-1 pos-number-2 pos-number-3; Not required; Default = .33 .66 1.0. -d (algorithm data file) File used to pass data from algorithm system to graphics generation system. syntax: -d string; Required; No default. -debug (produce debugging messages) Causes system debug messages to be printed. syntax: -debug (boolean switch); Not required; Default = off. -ebar (error bar mode) Determines how error bars are printed on time series graphs. Values: 0 = no error bars. 1 = error bars printed above graph. 2 = error bars printed below graph. 3 = error bars printed both above and below. 4 = error bars towards middle of graph. 5 = error bars away from middle of graph. syntax: -ebar non-neg-integer; Not required; Default = 3. -fontsizegeneral (general print fontsize) Size in points of font used for non-titles in graphics. syntax: -fontsizegeneral pos-integer; Not required; Default = 14. -fontsizetitle (fontsize for titles) Size in points of font used for titles in graphics. syntax: -fontsizetitle pos-integer; Not required; Default = 16. -gf (graphics file prefix) Output postscript graphics file prefix. File name suffix depends on graphics mode ("-gmode"). If "-gmode" = 1, suffix = optimal path number + ".ps". If ("-gmode") = 2, suffix = optimal path number + a, b, c, and d + ".ps". If not provided, output file name (with suffixes) is used. syntax: -gf string; Not required; No default. -gmode (graphics mode) Graphical output mode. Four diagrams are produced: Diagrams of both input time series, optimal path discovered by algorithm, and diagram of aligned time series. Graphics mode 1 = four diagrams produced on one (one graphical output file) each 1/4 size. Graphics mode 2 = four separate pages (separate files) produced at full size. syntax: -gmode pos-integer; Not required; Default = 1. -gridgray (path graph gray level) Path graph gray level: 0 = black, 1 = white. syntax: -gridgray non-neg-number; Not required; Default = 0.5. -height (graphic height) Height in inches of output graphic syntax: -height pos-number; Not required; Default = 10.5. -labelpathgraph (label path graph) Determines whether path graph axes will be labeled with time point numbers. syntax: -labelpathgraph (boolean switch); Not required; Default = on. -o (output file name) Output message file; STDOUT if not specified. syntax: -o string; Required; No default. -p (parameter file name) Allows parameters to be provided in file. syntax: -p string; Not required; No default. -scaseignore (ignore selection case) When provided, ignores case when matching features specified in "-selection" file against algorithm data file ("-d"). syntax: -scaseignore (boolean switch); Not required; Default = on. -selection (gene selection file) Selection of genes in algorithm data file ("-d") that will be graphed. File syntax: gene-name for each individual gene to graph. //GROUP group-name gene-name1 gene-name2 ... gene-namen // for each group to be graphed via a summary graph. Last line in file must end with a newline (\n) character. If not provided, entire "-d" file is graphed either as indivdiual genes or as summary graph depending on "-smode" parameter. syntax: -selection string; Not required; No default. -sizedash (dash size) Size in points of dashes for dashed lines in graphics. syntax: -sizedash non-neg-integer; Not required; Default = 3. -smode (selection mode) Selection mode. Processed only when "-selection" file not provided. Under these circumstances, all genes in "-d" file are graphed. When "-smode" = 1, all genes are graphed individually. When "-smode" = 2, all genes are graphed in one summary graph. syntax: -smode pos-integer; Not required; Default = 1. -timeticsize (time series ticmark size) Size of time ticmarks as fraction of minimum of "-height" and "-width" sizes. syntax: -timeticsize pos-number; Not required; Default = .02. -width (graphic width) Width in inches of output graphic syntax: -width pos-number; Not required; Default = 7.5. -xaxistimeprecision (precision of times printed on x axis) Number of significant digits of time labels. syntax: -xaxistimeprecision pos-integer; Not required; Default = 1. -xhatchsize (x axis hatchmark size) Size of x axis hatchmarks as fraction of "-height". syntax: -xhatchsize pos-number; Not required; Default = .01. -xtimelabelfreq (frequency of x axis time labels) Determines how often time labels are printed. 0 = not printed, 1 = all are printed, 2 = every other label printed, etc. syntax: -xtimelabelfreq non-neg-integer; Not required; Default = 1. -yfeatrangelabels (print feature range labels) Determines whether feature range labels will be printed. syntax: -yfeatrangelabels (boolean switch); Not required; Default = on. -yfeatrangelines (draw feature range labels) Determines whether feature range lines will be drawn. Turning this off also suppresses feature range labels for range boundary lines. syntax: -yfeatrangelines (boolean switch); Not required; Default = on. -yfeatrangeprecision (precision of feature range labels) Number of significant digits of feature range labels. Range labels are rounded to this precision. syntax: -yfeatrangeprecision pos-integer; Not required; Default = 2. -yhatchsize (y axis hatchmark size) Size of y axis hatchmarks as fraction of "-width". syntax: -yhatchsize pos-number; Not required; Default = .008.