; Comment: any line starting with a ';' is a comment. Resolution: <integer> ; Default is 300, don't change this. PagesWide: <integer> ; Number of pages that a panel spans. Default is 1 PagesHigh: <integer> ; Number of pages that contain panels. Default is 1 Background: <color> ; Color used for background. Default is white (255,255,255) Foreground: <color> ; Color used for labels, scales, etc. Default is black (0,0,0) LabelPages: <integer> ; Default 0, whether to place a page number in the lower left margin. LabelFirstMargin: <integer> ; Default 0, whether to place label in the first margin on a page. LabelLastMargin: <integer> ; Default 0, whether to place label in the last margin on a page. LabelLeftMargin: <integer> ; Default 0, whether to place label in the left margins on a page. LabelRightMargin: <integer> ; Default 0, whether to place label in the right margins on a page. SplitFile: <integer> ; Default 0, whether to split each page into a seperate file. Rotate: <integer> ; Default 0, whether to rotate the plot. Centerfold: <integer> ; Default 0, whether to leave room for staple in the center of an overlapped ; plot. OverLap: <integer> ; Default 0, whether to continue plotting into the margin on panel that ; cross page boundaries. PanelGroupsPerPage: <integer> ; Default 1, number of panel groups per page. GraphStart: <integer> ; Default 0, start of graph GraphEnd: <integer> ; Default 0, end of graph ; The start and end of graph determine how much space will be taken ; up by the graph and there is room for labels at the beginning or end. GenomeStart: <integer> ; Default 0, start of genome. GenomeEnd: <integer> ; Default 0, end of genome. ; The start and end of genome determines where the axes start and stop. PageWidth: <real> ; default 8.5 in, width of page PageHeight: <real> ; default 11 in, length of page Circular: <int> ; default 0, whether to make a circular or linear plot. Legend: <int> ; default 0, whether to include a legend on a circular plot. InsideRadius: <real> ; default 1.5, inside radius of circular plot OutsideRadius: <real> ; default 1.5, outside radius of circular plot TopMargin: <real> BottomMargin: <real> LeftMargin: <real> RightMargin: <real> ; default 0.5 in, margin sizes LabelScale: <real> ; default 1, scale factor to enlarge or reduce labels. LabelBaseline: <real> ; default 0.5, determines the font baseline wrt the panel. ; 0.0 specifies the baseline at the bottom of the panel. ; 0.5 specifies the baseline at the center of the panel. ; 1.0 specifies the baseline at the top of the panel. TextPriority: <integer> ; default 9, text with priority 1 through n get printed. Panel: <weight> blank Panel: <weight> histogram histogram.xls [<min> <max> [<clipmin> <clipmax>]] Panel: <weight> arrow arrow.xls [<minlength>] Panel: <weight> <clipmax>]]] Panel: <weight> Panel: <weight> Panel: <weight> <end>]] xyplot xy.xls <color> [<width> [<min> <max> [<clipmin> text text.xls [<align> [<prio>]] scale <majortick> <minortick> [<width>] demarcation demarcation.xls <color> [[<width>] [<start> min, max (real): Minimum and Maximum y values plotted. Default: min and max autoscale with the data if not set. color: RGB triple indicating color width (integer): width of lines (recommended minimum value:2) Default: 2 align (integer): -1 left, 0 center, 1 right for linear plot -1 down radially, 0 arc, 1 up radially for circular plot Default: 0 prio (integer): 1 highest, 2 second, ... Default: 1 majortick (integer): big tick mark and label placed every majortick units. minortick (integer): small tick mark placed every minortick units. start, end (real): what panel weight to start and end demarcation. minlength (integer): minimum length of arrows in base pairs. Label: <Some text string> ; Label placed next to panel at beginning and/or end of genome. MarginLabel: <Some text string> ; Label placed next to panel in the margins. LegendStart: <integer> ; default 0; where to start the legend for this panel in circular plots. TextPanel: <weight> blank TextPanel: <weight> text TextLabel: <Some text string> ; Label placed int the panel in the middle of the circular plot. StartLegend: legend.xls <rows> <cols> [<boxheight>] EndLegend: legend.xls <rows> <cols> [<boxheight>] rows, cols (integer): Number of rows and colums in the legend. boxheight (real): Fraction of column height which the box occupies Default: 1.0