Bio::G...w_gene(3pm)

✨ Bio::Graphics::Glyph::gene ✨

okay so bestie, welcome to the manual page for Bio::Graphics::Glyph::gene (she's a 3pm Perl doc, one of the User Contributed ones, and yes her full name is Bio::Graphics::Glyph::gene(3pm) — the header up top just truncates her bc she's long 💅).

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🌸 NAME 🌸

Bio::Graphics::Glyph::gene — a GFF3-compatible gene glyph 🧬✨

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🎀 SYNOPSIS 🎀

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

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🦋 DESCRIPTION 🦋

So this glyph is the one you call when you're drawing genes that might have alternatively-spliced transcripts. The different isoforms get stacked on top of each other, and the whole stack shares one single label and one single description. Each individual transcript's name can optionally be printed to the left of the transcript glyph, if you want. 🫶

The transcripts (aka splice isoforms) are drawn using the processed_transcript glyph. CDS features get drawn in the background color, and the UTRs get drawn in an alternate color that you pick with the utr_color option. Bonus: you can make the UTRs thinner than the CDS by setting the "thin_utr" option. Obsessed. 😌

This glyph is literally designed to work properly with GFF3-style three-tier genes, where:

• the top level feature has the Sequence Ontology type of "gene"
• the second level feature(s) have the SO type "mRNA"
• 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 too (like exon, intron, translation), but rn they're currently ignored unless you supply the sub_part option. And if you do use the sub_part option, that feature type gets used and the CDS and UTR features get excluded. So like, you could use that to say "actually use exons instead" — that's the whole vibe. 🎯

Also! This glyph is a subclass of processed_transcript, and it recognizes the same options. Slay.

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✨ OPTIONS ✨

The following options are standard among all Glyphs. For a full explanation, go see Bio::Graphics::Glyph. 👑

• -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: undef (false)
• -connector_color — connector color. Default: black
• -label — whether to draw a label. Default: undef (false)
• -description — whether to draw a description. Default: undef (false)
• -strand_arrow — whether to indicate strandedness. Default: undef (false)
• -hilite — highlight color. Default: undef (no color)

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In addition, the gene glyph recognizes these glyph-specific options 💅:

• -label_transcripts — flag. If true, then the display name of each transcript will be drawn to the left of the transcript glyph. Default: undef (false)
• -thin_utr — flag. If true, UTRs will be drawn at 2/3 of the height of CDS segments. Default: undef (false)
• -utr_color — color of UTR segments. Default: Gray #D0D0D0
• -decorate_introns — draw strand with little arrows on the intron. Default: undef (false)

⚠️ heads up bestie: the -adjust_exons and -implied_utrs options are inherited from processed_transcript, but they are quietly ignored here. If you want that type of processing, please use the processed_transcript glyph itself. no cap.

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💀 BUGS 💀

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

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🌈 SEE ALSO 🌈

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>

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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and that's the whole page, bestie 🫶 this one's perl v5.30.0, dated 2019-11-25, and it lives under the manual name Bio::G...w_gene(3pm) (yes the name got cut off, she's just that iconic 💅✨). mwah, go draw some genes 🧬💖