; 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