NAME

Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph

SYNOPSIS

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

DESCRIPTION

This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other and given a single label and description that apply to the entire stack. Each individual transcript's name is optionally printed to the left of the transcript glyph.

Transcripts (splice isoforms) are drawn using the processed_transcript glyph. CDS features are drawn in the background color, and the UTRs are drawn in an alternate color selected by the utr_color option. In addition, you can make the UTRs thinner than the CDS by setting the "thin_utr" option.

This glyph is designed to work properly with GFF3-style three-tier genes, in which the top level feature has the Sequence Ontology type of "gene", the second level feature(s) have the SO type "mRNA", and the third level feature(s) have the SO type "CDS", "five_prime_utr" and "three_prime_utr." Subparts named "UTR" are also honored. The feature can contain other subparts as well (e.g. exon, intron, translation), but they are currently ignored unless the option sub_part is supplied. If the sub_part option is used that feature type will be used and CDS and UTR features will be excluded. This could be used for specifying that exons be used instead, for example.

This glyph is a subclass of processed_transcript, and recognizes the same options.

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                 undef (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label        undef (false)

  -description  Whether to draw a description  undef (false)

  -strand_arrow Whether to indicate            undef (false)
                 strandedness

  -hilite       Highlight color                undef (no color)

In addition, the gene glyph recognizes the following glyph-specific options:

  Option         Description                   Default
  ------         -----------                   -------

  -label_transcripts                           undef (false)
                 Flag. If true, then the
                 display name of each
                 transcript will be drawn
                 to the left of the transcript
                 glyph.

  -thin_utr      Flag.  If true, UTRs will      undef (false)
                 be drawn at 2/3 of the
                 height of CDS segments.

  -utr_color     Color of UTR segments.         Gray #D0D0D0

  -decorate_introns
                 Draw strand with little arrows undef (false)
                 on the intron.

The -adjust_exons and -implied_utrs options are inherited from processed_transcript, but are quietly ignored. Please use the processed_transcript glyph for this type of processing.

BUGS

The SO terms are hard-coded. They should be more flexible and should recognize ISA relationships.

AUTHOR

Lincoln Stein <lstein@cshl.org>