Bio::G...ph::dna(3pm)

💖 NAME 💖

Bio::Graphics::Glyph::dna — bestie, this is the "dna" glyph. That's it, that's the name. Iconic.

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✨ SYNOPSIS ✨

Lowkey the whole vibe is just:

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

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🧬 DESCRIPTION 🧬

Okay so this glyph draws DNA sequences. Periodt.

• At high magnifications, this glyph will draw the actual base pairs of the sequence — both strands, fr fr.
• At low magnifications, the glyph will plot the GC content.

By default, the GC calculation will use non-overlapping bins, but this can be changed by specifying the gc_window option — and in that case, a sliding window calculation will be used. Slay.

For this glyph to work, the feature must return a Bio::PrimarySeq DNA object in response to the seq() method. No cap. For example, you can use a Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq like this:

my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end => 800 );
$feature->attach_seq($dna);
$panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used. 💅

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🌸 OPTIONS 🌸

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. (Yes bestie, this is the universal starter pack.)

• -fgcolor — Foreground color. Default: black
• -outlinecolor — Synonym for -fgcolor
• -bgcolor — Background color. Default: turquoise
• -fillcolor — Synonym for -bgcolor
• -linewidth — Line width. Default: 1
• -height — Height of glyph. Default: 10
• -font — Glyph font. Default: gdSmallFont
• -connector — Connector type. Default: 0 (false)
• -connector_color — Connector color. Default: black
• -label — Whether to draw a label. Default: 0 (false)
• -description — Whether to draw a description. Default: 0 (false)
• -hilite — Highlight color. Default: undef (no color)

In addition to the common options, the following glyph-specific options are recognized — this is the main character section, honestly:

• -do_gc — Whether to draw the GC graph at low mags. Default: true
• -gc_window — Size of the sliding window to use in the GC content calculation. If this is not defined, non-overlapping bins will be used. If this is set to "auto", then the glyph will choose a window equal to 1% of the interval. Default: <none>
• -gc_bins — Fixed number of intervals to sample across the panel. Default: 100
• -axis_color — Color of the vertical axes in the GC content graph. Default: fgcolor
• -strand — Show both forward and reverse strand, one of "forward", "reverse", "both" or "auto". In "auto" mode, +1 strand features will show the plus strand, -1 strand features will show the reverse complement, and strandless features will show both. Default: auto

⭐ NOTE: -gc_window=>'auto' gives nice results and is recommended for drawing GC content. The GC content axes draw slightly outside the panel, so you may wish to add some extra padding on the right and left. Heads up bestie, plan your layout accordingly 🫶

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😭 BUGS 😭

Please report them. (That's the whole section. Not me being dramatic, that's literally what it says.)

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🦋 SEE ALSO 🦋

Go read these, bestie — the whole friend group:

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

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👑 AUTHOR 👑

Lincoln Stein <lstein@cshl.org>.

Sliding window GC calculation added by Peter Ashton <pda@sanger.ac.uk>. We stan a contributor 💜

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.

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okay that's the whole page, bestie — no cap, you're officially a DNA-glyph girlie now 💖✨

This was Bio::G...ph::dna(3pm) from the User Contributed Perl Documentation, perl v5.30.0, dated 2019-11-25. mwah, go draw some sequences 🧬🎀