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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Graphics::Glyph::decorated_transcript \- draws processed transcript with protein decorations .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& See L and L. .Ve .SH "DESCRIPTION" .IX Header "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 \s-1CDS\s0 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. .PP Protein decorations are provided either with mRNA features inside \s-1GFF\s0 files (see example below) or dynamically via callback function using the \fBadditional_decorations\fR option (see glyph options). The following line is an example of an mRNA feature in a \s-1GFF\s0 file that contains two protein decorations, one signal peptide predicted by SignalP and one transmembrane domain predicted by \s-1TMHMM:\s0 .PP \&\f(CW\*(C`chr1 my_source mRNA 74796 75599 . + . ID=rna_gene\-1;protein_decorations=SignalP40:SP:1:23:0:my_comment,TMHMM:TM:187:209:0\*(C'\fR .PP Each protein decoration consists of six fields separated by a colon: .IP "1. type" 4 .IX Item "1. type" Decoration type. For example used to specify decoration source (e.g. 'SignalP40') .IP "2. name" 4 .IX Item "2. name" Decoration name. Used as decoration label by default (e.g. '\s-1SP\s0' for signal peptide) .IP "3. start" 4 .IX Item "3. start" Start coordinate at the protein-level (1\-based coordinate) .IP "4. end" 4 .IX Item "4. end" End coordinate at the protein-level .IP "5. score" 4 .IX Item "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). .IP "6. description" 4 .IX Item "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 \s-1GFF\s0 tag parser should be avoided. .PP 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 \s-1CDS\s0 feature, but each time with a different decoration that overlaps with this \s-1CDS.\s0 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: .IP "\(bu" 4 type \-\-> \f(CW$glyph\fR\->active_decoration\->type .IP "\(bu" 4 name \-\-> \f(CW$glyph\fR\->active_decoration\->name .IP "\(bu" 4 nucleotide start coordinate \-\-> \f(CW$glyph\fR\->active_decoration\->start .IP "\(bu" 4 nucleotide end coordinate \-\-> \f(CW$glyph\fR\->active_decoration\->end .IP "\(bu" 4 protein start coordinate \-\-> \f(CW$glyph\fR\->active_decoration\->get_tag_values('p_start') .IP "\(bu" 4 protein end coordinate \-\-> \f(CW$glyph\fR\->active_decoration\->get_tag_values('p_end') .IP "\(bu" 4 score \-\-> \f(CW$glyph\fR\->active_decoration\->score .IP "\(bu" 4 description \-\-> \f(CW$glyph\fR\->active_decoration\->description .PP In addition, the glyph passed to the callback allows access to the parent glyph and parent feature if required (use \f(CW$glyph\fR\->parent or \f(CW$glyph\fR\->parent\->feature). .SS "\s-1OPTIONS\s0" .IX Subsection "OPTIONS" This glyph inherits all options from the Bio::Graphics::Glyph::processed_transcript glyph. In addition, it recognizes the following glyph-specific options: .PP .Vb 2 \& 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 \& 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 \*(Aqtransparent\*(Aq can be used here in \& combination with the option \*(Aqdecoration_border\*(Aq to \& draw decorations as outlines. \& \& \-decoration_border \& \& Decoration border style. By default, decorations are 0 (none) \& drawn without border (\*(Aqnone\*(Aq or 0). Other valid \& options here include \*(Aqsolid\*(Aq or \*(Aqdashed\*(Aq. \& \& \-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 \& \*(Aqinside\*(Aq decorations (default) or \*(Aqabove\*(Aq and \*(Aqbelow\*(Aq \& 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. .Ve .SH "BUGS" .IX Header "BUGS" Strandedness arrows are decorated incorrectly. Currently, the glyph plots a rectangular box over the arrow instead of properly coloring the arrow. .PP 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. .PP For \s-1SVG\s0 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. .PP Please report all errors. .SH "SEE ALSO" .IX Header "SEE ALSO" Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::decorated_gene, Bio::Graphics::Glyph::processed_transcript .SH "AUTHOR" .IX Header "AUTHOR" Christian Frech .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See \s-1DISCLAIMER\s0.txt for disclaimers of warranty.