NAME

Bio::Graphics::Glyph::decorated_transcript - draws processed transcript with protein decorations

SYNOPSIS

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

DESCRIPTION

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 additional_decorations 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:

1. type: Decoration type. For example used to specify decoration source (e.g. 'SignalP40')
2. name: Decoration name. Used as decoration label by default (e.g. 'SP' for signal peptide)
3. start: Start coordinate at the protein-level (1-based coordinate)
4. end: End coordinate at the protein-level
5. score: 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).
6. description: 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.

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:

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

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).

OPTIONS

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
------ ----------- -------

-decoration_visible

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_color

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

Decoration border style. By default, decorations are 0 (none)
drawn without border ('none' or 0). Other valid
options here include 'solid' or 'dashed'.

-decoration_border_color

Color of decoration border. black

-decoration_label

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.

-decoration_label_position

Position of decoration label. Labels can be drawn inside
'inside' decorations (default) or 'above' and 'below'
decorations.

-decoration_label_color

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

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

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.

-decoration_position

Currently decorations can only be drawn inside inside
CDS segments.

-flip_minus

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
structure comparisons.

BUGS

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 set.

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.

AUTHOR

Christian Frech <cfa24@sfu.ca>