NAME

Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph

SYNOPSIS

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

DESCRIPTION

This glyph draws a cladogram for any set of species along with their alignment data in relation to the reference species. At high magnification, base pair alignements will be displayed. At lower magnification, a conservation score plot will be drawn. Gaps as specified by CIGAR are supported. Currently the scores are drawn to a log plot with the restriction that the score will be the same across all base pairs within an alignment. It is hoped that this restriction can be addressed in the future.

For this glyph to work, the feature must return a DNA sequence string in response to the dna() method. Also, a valid tree file must be available in a format readable by the Bio::Tree library.

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
  ------      -----------               -------

  -draw_clado_left
              Draws the Cladogram on left 0

  -species_spacing
              Spacing of species in DNA   1
              mode in units of font height

  -species_spacing_score
              Spacing of spcies in        5
              conservation view in units
              of font height

  -hide_label Whether to label spcies     0

  -tree_file  Path of file containing     undef
              cladogram tree information
  -tree_format Format of tree file         newick

  -axis_color Color of the vertical axes  fgcolor
              in the GC content graph

  -errcolor   Color of all misalignment   fgcolor
              indicators

  -mid_axis_color
              Color of the middle axis of
              the conservation score graph axis_color

  -clado_bg  Color of the clado bg       bgcolor
              indicators

  -ref_color  Color of base pair bg for   bgcolor
              the reference sequence

  -targ_color Color of base pair bg for   bgcolor
              all base pairs that match
              reference

BUGS

Please report them.

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

AUTHORS

Hisanaga Mark Okada Lincoln Stein <lstein@cshl.org>.