Lincoln D. Stein > Bio-Graphics-2.35 > Bio::Graphics::Glyph::arrow

Download:
Bio-Graphics-2.35.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  12
Open  1
View/Report Bugs
Source   Latest Release: Bio-Graphics-2.37

NAME ^

Bio::Graphics::Glyph::arrow - the "arrow" glyph

SYNOPSIS ^

  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION ^

This 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.

OPTIONS

The 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

  arrow(-scale=>100);

will draw tick marks labelled appropriately to your external scale.

BUGS ^

Please report them.

SEE ALSO ^

Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHOR ^

Lincoln Stein <lstein@cshl.org>.

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.

syntax highlighting: