Manual Reference Pages - BIO::GRAPHICS::GLYPH::DECORATED_TRANSCRIPT (3)
Bio::Graphics::Glyph::decorated_transcript - draws processed transcript with protein decorations
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript glyph
and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes
inside or around CDS segments. Protein decorations are specified at the mRNA transcript level
in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph.
Decorations are allowed to span exon-exon junctions, in which case decorations are split between exons.
By default, the glyph automatically assigns different colors to different types of protein decorations, whereas
decorations of the same type are always assigned the same color.
Protein decorations are provided either with mRNA features inside GFF files (see example below) or
dynamically via callback function using the <B>additional_decorationsB> option (see glyph options).
The following line is an example of an mRNA feature in a GFF file that contains two protein decorations,
one signal peptide predicted by SignalP and one transmembrane domain predicted by TMHMM:
chr1 my_source mRNA 74796 75599 . + . ID=rna_gene-1;protein_decorations=SignalP40:SP:1:23:0:my_comment,TMHMM:TM:187:209:0
Each protein decoration consists of six fields separated by a colon:
If callback functions are used as glyph parameters (see below), the callback is called for each
decoration separately. That is, the callback can be called multiple times for a given CDS feature,
but each time with a different decoration that overlaps with this CDS. The currently drawn (active)
decoration is made available to the callback via the glyph method active_decoration. The active
decoration is returned in form of a Bio::Graphics::Feature object, with decoration data fields
mapped to corresponding feature attributes in the following way:
Decoration type. For example used to specify decoration source (e.g. SignalP40)
Decoration name. Used as decoration label by default (e.g. SP for signal peptide)
Start coordinate at the protein-level (1-based coordinate)
End coordinate at the protein-level
Optional. Score associated with a decoration (e.g. Pfam E-value). This score can be used
to dynamically filter or color decorations via callbacks (see glyph options).
Optional. User-defined description of decoration. The glyph ignores this description,
but it will be made available to callback functions for inspection. Special characters
like : or , that might interfere with the GFF tag parser should be avoided.
In addition, the glyph passed to the callback allows access to the parent glyph and
parent feature if required (use $glyph->parent or $glyph->parent->feature).
type --> $glyph->active_decoration->type
name --> $glyph->active_decoration->name
nucleotide start coordinate --> $glyph->active_decoration->start
nucleotide end coordinate --> $glyph->active_decoration->end
protein start coordinate --> $glyph->active_decoration->get_tag_values(p_start)
protein end coordinate --> $glyph->active_decoration->get_tag_values(p_end)
score --> $glyph->active_decoration->score
description --> $glyph->active_decoration->description
This glyph inherits all options from the Bio::Graphics::Glyph::processed_transcript glyph.
In addition, it recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------
Specifies whether decorations should be visible false
or not. For selective display of individual
decorations, specify a callback function and
return 1 or 0 after inspecting the active decoration
of the glyph.
Decoration background color. If no color is <auto>
specified, colors are assigned automatically by
decoration type and name, whereas decorations of
identical type and name are assigned the same color.
A special color transparent can be used here in
combination with the option decoration_border to
draw decorations as outlines.
Decoration border style. By default, decorations are 0 (none)
drawn without border (none or 0). Other valid
options here include solid or dashed.
Color of decoration border. black
Decoration label. If not specified, the second data true
field of the decoration is used as label. Set this (decoration name)
option to 0 to get unlabeled decorations. If the label
text extends beyond the size of the decorated segment,
the label will be clipped. Clipping does not occur
for SVG output.
Position of decoration label. Labels can be drawn inside
inside decorations (default) or above and below
Decoration label color. If not specified, this color
is complementary to decoration_color (e.g., yellow text
on blue background, white on black, etc.). If the
decoration background color is transparent and no
decoration label color is specified, the foreground color
of the underlying transcript glyph is used as default.
Additional decorations to those specified in the GFF undefined
file. Expected is a string in the same format as
described above for GFF files.
This parameter is intended to be used as callback
function, which inspects the currently processed
transcript feature (first parameter to callback)
and returns additional protein decorations that
should be drawn.
Decoration height. Unless specified otherwise, CDS height-2
the height of the decoration is the height of the
underlying transcript glyph minus 2, such that
the decoration is drawn within transcript boundaries.
Currently decorations can only be drawn inside inside
If set to 1, features on the negative strand will be false
drawn flipped. This is not particularly useful in
GBrowse, but becomes handy if multiple features should
be drawn within the same panel, left-aligned, and on
top of each other, for example to allow for easy gene
Strandedness arrows are decorated incorrectly. Currently, the glyph plots a rectangular box
over the arrow instead of properly coloring the arrow.
Overlapping decorations are drawn on top of each other without particular order. The only
solution to this problem at this point is to reduce decorations to a non-overlapping
For SVG output or if drawn not inside decorations, decoration labels are not clipped.
Similar as for overlapping decorations, this can result in labels being drawn on top
of each other.
Please report all errors.
Christian Frech <firstname.lastname@example.org>
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.
|perl v5.20.3 ||BIO::GRAPHICS::GLYPH::DECORATED_TRANSCRIPT (3) ||2016-04-05 |
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