Provided by: libbio-graphics-perl_2.40-2_all bug

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.

SEE ALSO

       Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::decorated_gene,
       Bio::Graphics::Glyph::processed_transcript

AUTHOR

       Christian Frech <cfa24@sfu.ca>

       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 v5.26.0                                2017-0Bio::Graphics::Glyph::decorated_transcript(3pm)