Bio-Graphics

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lib/Bio/Graphics/Glyph/merged_alignment.pm  view on Meta::CPAN

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.

=head2 SAMPLE CONFIGURATION

Sample gbrowse configuration stanzas for an alignment feature
using this glyph.  The scores are assumed to be expressed 
as percent identity (0-100).

 # base configuration
 [BLASTZ]
 feature      = blastz_alignment
 glyph        = merged_alignment
 bincolors    = #A0A0A0 powderblue cornflowerblue blue
 bins         = 60-70 70-80 80-90 90-100
 category     = Sequence Similarity Tracks
 height       = 6
 bump         = 1

lib/Bio/Graphics/Glyph/xyplot.pm  view on Meta::CPAN

use Bio::Root::Version;
our $VERSION = ${Bio::Root::Version::VERSION};

use constant DEBUG=>0;
use constant EXTRA_LABEL_PAD=>8;

sub my_description { 
    return <<'END';
This glyph is used for drawing features that have a position on the
genome and a numeric value.  It can be used to represent gene
prediction scores, motif-calling scores, percent similarity,
microarray intensities, or other features that require a line plot.

The plot is designed to work on a single feature group that contains
subfeatures. It is the subfeatures that carry the score
information. For a more efficient implementation that is suitable for
dense genome-wide data, use Bio::Graphics::Wiggle and the
wiggle_xyplot glyph.
END

}

lib/Bio/Graphics/Glyph/xyplot.pm  view on Meta::CPAN

Bio::Graphics::Glyph::xyplot - The xyplot glyph

=head1 SYNOPSIS

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

=head1 DESCRIPTION

This glyph is used for drawing features that have a position on the
genome and a numeric value.  It can be used to represent gene
prediction scores, motif-calling scores, percent similarity,
microarray intensities, or other features that require a line plot.

The X axis represents the position on the genome, as per all other
glyphs.  The Y axis represents the score.  Options allow you to set
the height of the glyph, the maximum and minimum scores, the color of
the line and axis, and the symbol to draw.

The plot is designed to work on a single feature group that contains
subfeatures.  It is the subfeatures that carry the score
information. The best way to arrange for this is to create an

lib/Bio/Graphics/Panel.pm  view on Meta::CPAN

     r,g,b,a       - red, green, blue, alpha
     blue:alpha    - symbolic name and alpha
     rgb(r,g,b)    - CSS style rgb values
     rgba(r,g,b,a) - CSS style rgba values

Alpha values can be specified as GD style integers ranging from 0
(opaque) to 127 (transparent), or as CSS-style floating point numbers
ranging from 0.0 (transparent) through 1.0 (opaque). As a special
case, a completely transparent color can be specified using the color
named "transparent". In the rgb() and rgba() forms, red, green, blue
values can be specified as percentages, as in rgb(100%,0%,50%);
otherwise, the values are integers from 0 to 255.

In addition, the -fgcolor and -bgcolor options accept the special
color names "featureScore" and "featureRGB". In the first case,
Bio::Graphics will examine each feature in the track for a defined
"score" tag (or the presence of a score() method) with a numeric value
ranging from 0-1000. It will draw a grayscale color ranging from
lightest (0) to darkest (1000). If the color is named "featureRGB",
then Bio::Graphics will look for a tag named "RGB" and will use that
as the color.