See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTIONThis glyph draws arrows. Depending on options, the arrows can be labeled, be oriented vertically or horizontally, or can contain major and minor ticks suitable for use as a scale.
OPTIONSThe following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default ------ ----------- ------- -fgcolor Foreground color black -outlinecolor Synonym for -fgcolor -bgcolor Background color turquoise -fillcolor Synonym for -bgcolor -linewidth Line width 1 -height Height of glyph 10 -font Glyph font gdSmallFont -connector Connector type 0 (false) -connector_color Connector color black -label Whether to draw a label 0 (false) -description Whether to draw a description 0 (false) -hilite Highlight color undef (no color)
In addition to the common options, the following glyph-specific options are recognized:
Option Description Default ------ ----------- ------- -tick Whether to draw major 0 and minor ticks. 0 = no ticks 1 = major ticks 2 = minor ticks -tickcolor Color to use for tick marks fgcolor -tickwidth Line width to use for ticks linewidth -parallel Whether to draw the arrow 1 (true) parallel to the sequence or perpendicular to it. -northeast Force a north or east 1 (true) arrowhead(depending on orientation) -east synonym of above -southwest Force a south or west 1 (true) arrowhead(depending on orientation) -west synonym of above -double force-doubleheaded arrow 0 (false) -base Draw a vertical base at the 0 (false) non-arrowhead side -scale Reset the labels on the arrow 0 (false) to reflect an externally established scale. -arrowstyle "regular" to create a simple regular arrowhead. "filled" to create a thick filled arrowhead -relative_coords use relative coordinates 0 (false) for scale -relative_coords_offset set the relative offset 1 for scale -label_intervals 0 (false) Put the numeric labels on the intervals between the ticks rather than on the ticks themselves. -units add units to the tick labels none e.g. bp -unit_divider 1 divide tick labels by the indicated amount prior to displaying (use, for example if you want to display in cR units)
Set -parallel to 0 (false) to display a point-like feature such as a polymorphism, or to indicate an important location. If the feature start == end, then the glyph will draw a single arrow at the designated location:
Otherwise, there will be two arrows at the start and end:
^ ^ | |
Scale: Pass in a externally established scale to reset the labels on the arrow. This is particularly useful for manually constructed images where the founding parameters of the panel are not 1-based. For example, a genetic map interval ranging from 0.1 - 0.3 can be constructed by first multiplying every value by 100. Passing
will draw tick marks labelled appropriately to your external scale.
BUGSPlease report them.
AUTHORLincoln Stein <[email protected]>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.