man Bio::Graphics::Glyph::graded_segments (3): The graded

SYNOPSIS

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

DESCRIPTION

This is identical to the ``alignment'' glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is proportionate to the score.

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, the alignment glyph recognizes the following glyph-specific options:

  Option      Description                   Default
  ------      -----------                   -------
  -max_score  Maximum value of the          Calculated
              feature's "score" attribute
  -min_score  Minimum value of the          Calculated
              feature's "score" attribute
  -vary_fg    Vary the foreground color as  0 (false)
              well as the background
  -merge_parts                             0 (false)
              Whether to simplify the
              alignment at low magnification
  -max_gap    Do not merge across gaps     Calculated
              that exceed this threshold

If max_score and min_score are not specified, then the glyph will calculate the local maximum and minimum scores at run time. Since many scoring functions are exponential you may wish to take the log of your scores before passing them to this glyph.

Simplifying the display of alignment features for large segments

The ``merge_parts'' option is used for semantic zooming. Specifically, if features are small and dense, they will not be displayed very well for large segments and the color-coding will be lost. If merge-parts is set to a true value, adjacent alignment parts will be merged until a gap exceeding a calculated or user-specified value is encountered. Unless specified, the maximum gap allowed for merging adjacent features is calculated as (L/10000)*(L/500), where L = the length of the sequence displayed in the browser. The exponentially increasing gap threshold allows more aggressive merging of alignment features as the size of the displayed sequence grows larger.

The score of the merged feature is calculated as a weighted average. For example, consider two adjacent HSPs that are each 400 bp in length and have scores of 60% and 70%. If the merge_parts option is set to a true value, the two HSPs would be merged in the display to a single 800 bp alignment block with an average score of 65%.

The merge_parts option is turned off by default.

BUGS

Please report them.

AUTHOR

Lincoln Stein <[email protected]>