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

✨ NAME ✨

Bio::Graphics::Glyph::phylo_align — the "phylogenetic alignment" glyph 💖 (yes bestie, this is the Bio::G...o_align(3pm) page you were looking for, we're just gonna be cute about it)

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🦋 SYNOPSIS 🦋

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

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🌸 DESCRIPTION 🌸

Okay so picture this: this glyph draws a cladogram for any set of species, and it pulls up their alignment data right next to it, all in relation to the reference species. Iconic behaviour honestly. 🧚

When you zoom all the way in (high magnification), you get the actual base pair alignments displayed. When you zoom out (lower magnification), it switches to drawing a conservation score plot instead. And yes, gaps as specified by CIGAR are supported — we love a format that plays nice. 💅

Right now the scores get drawn to a log plot, with one little restriction: the score will be the same across all base pairs within an alignment. The hope is that this restriction can be addressed in the future. Not me manifesting a future release… 🙈

Heads up bestie, for this glyph to work, two things have to be true: the feature must return a DNA sequence string in response to the dna() method, and a valid tree file must be available in a format readable by the Bio::Tree library. No tree, no slay. 🌳

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🎀 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)

So in vibes terms:

• -fgcolor — the foreground color, default black 🖤
• -outlinecolor — literally just a synonym for -fgcolor
• -bgcolor — background color, default turquoise 💎 (yes, turquoise, she's an icon)
• -fillcolor — synonym for -bgcolor, same energy
• -linewidth — how thicc the line is, default 1
• -height — height of the glyph, default 10
• -font — the 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:

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

And the girl-talk breakdown, one by one:

• -draw_clado_left — draws the cladogram on the left, default 0
• -species_spacing — spacing of species in DNA mode, measured in units of font height, default 1
• -species_spacing_score — spacing of species in the conservation view, measured in units of font height, default 5
• -hide_label — whether to label species, default 0
• -tree_file — path of the file containing the cladogram tree information, default undef
• -tree_format — format of the tree file, default newick
• -axis_color — color of the vertical axes in the GC content graph, default fgcolor
• -errcolor — color of all misalignment indicators, default fgcolor
• -mid_axis_color — color of the middle axis of the conservation score graph axis, default axis_color
• -clado_bg — color of the clado bg indicators, default bgcolor
• -ref_color — color of the base pair bg for the reference sequence, default bgcolor
• -targ_color — color of the base pair bg for all base pairs that match reference, default bgcolor

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💀 BUGS 💀

Please report them. (fr fr, just tell someone, don't suffer in silence bestie 🫶)

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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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👑 AUTHORS 👑

Hisanaga Mark Okada and 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 came from perl v5.30.0, dated 2019-11-25, and it's the Bio::G...o_align(3pm) manual page — go forth and align those phylogenies, you absolute main character. 🦋✨