Bio-Graphics
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lib/Bio/Graphics/Glyph/decorated_transcript.pm view on Meta::CPAN
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_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. 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 the same CDS feature,
but each time with a different decoration. 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).
END
}
sub my_options {
return {
decoration_visible => [
'boolean',
'false',
'Specifies whether decorations should be visible 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 => [
'color',
undef,
'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 \'transparent\' can be used here in combination with',
'the option \'decoration_border\' to draw decorations as outlines.'],
decoration_border => [
['none', 'solid', 'dashed'],
'none',
'Decoration border style. By default, decorations are drawn without border (\'none\' or',
'0). Other valid options here include \'solid\' or \'dashed\'.'],
decoration_border_color => [
'color',
'black',
'Color of decoration boder.'],
decoration_label => [
'string',
undef,
'Decoration label. If not specified, the second data field of the decoration is used',
'as label. Set this 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 => [
['inside', 'above', 'below'],
undef,
'Position of decoration label. Labels can be drawn \'inside\' decorations (default)',
'or \'above\' and \'below\' decorations.'],
decoration_label_color => [
'color',
'undef',
'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 => [
'string',
undef,
'Additional decorations to those specified in the GFF 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 => [
'integer',
undef,
'Decoration height. Unless specified otherwise, 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 => [
['inside'],
'inside',
'Currently, decorations can only be drawn inside CDS segments.'],
flip_minus => [
'boolean',
0,
'If set to 1, features on the negative strand will be 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 easy gene structure comparisons.'],
}
}
sub new {
my ( $class, @args ) = @_;
my %param = @args;
warn "new(): " . join( ",", @args ) . "\n" if (DEBUG == 2);
my $feature = $param{'-feature'};
my $factory = $param{'-factory'};
my $flip_minus = $factory->get_option('flip_minus');
if ( $flip_minus and $feature->strand < 1 ) {
for ( my $i = 0 ; $i < @args ; $i++ ) {
$args[ $i + 1 ] = 1 if ( $args[$i] eq '-flip' );
}
}
my $self = $class->Bio::Graphics::Glyph::processed_transcript::new(@args);
$self->{'parent'} = undef;
$self->{'additional_decorations'} = undef;
$self->{'active_decoration'} = undef;
$self->{'add_pad_bottom'} = undef;
# give sub-glyphs access to parent glyph's decorations
if ($self->decorations_visible)
{
foreach my $sub_glyph ( $self->parts ) {
$sub_glyph->{'parent'} = $self;
}
}
lib/Bio/Graphics/Glyph/decorated_transcript.pm view on Meta::CPAN
if ( !$decoration_height );
return $decoration_height;
}
sub decoration_position {
my $self = shift;
my $decoration = shift;
if (!$decoration)
{
$self->throw("decoration not specified") if (DEBUG);
return "inside";
}
$self->{'active_decoration'} = $decoration; # set active decoration for callback
my $decoration_position = $self->option('decoration_position');
$decoration_position = 'inside'
if ( !$decoration_position );
if ($decoration_position ne 'inside' and $decoration_position ne 'stacked_bottom')
{
$self->throw('invalid decoration_position: '.$decoration_position) if (DEBUG);
$decoration_position = 'inside';
}
return $decoration_position;
}
sub _hash {
my $hash = 0;
foreach ( split //, shift ) {
$hash = $hash * 33 + ord($_);
}
return $hash;
}
sub decoration_label_color {
my $self = shift;
my $decoration = shift;
if (!$decoration)
{
$self->throw("decoration not specified") if (DEBUG);
return "black";
}
$self->{'active_decoration'} = $decoration; # set active decoration for callback
my $decoration_label_color = $self->option('decoration_label_color');
return $decoration_label_color
if ( defined $decoration_label_color
and $decoration_label_color ne 'auto'
and $decoration_label_color ne '' );
my $decoration_color = $self->decoration_color($decoration);
return $self->fgcolor
if ((!$decoration_label_color or $decoration_label_color eq 'auto')
and $decoration_color eq "transparent");
# assign color complementary to decoration color
my ( $red, $green, $blue ) =
Bio::Graphics::Panel->color_name_to_rgb($decoration_color);
$decoration_label_color =
sprintf( "#%02X%02X%02X", 255 - $red, 255 - $green, 255 - $blue ); # background complement
return $decoration_label_color;
}
sub decoration_label {
my $self = shift;
my $decoration = shift;
if (!$decoration)
{
$self->throw("decoration not specified") if (DEBUG);
return "";
}
$self->{'active_decoration'} = $decoration; # set active decoration for callback
my $decoration_label = $self->option('decoration_label');
return undef
if ( defined $decoration_label and $decoration_label eq "0" );
return $decoration_label
if ( $decoration_label and $decoration_label ne "1");
# assign decoration name as default label
return $decoration->name;
}
sub decoration_label_position {
my $self = shift;
my $decoration = shift;
if (!$decoration)
{
$self->throw("decoration not specified") if (DEBUG);
return "";
}
$self->{'active_decoration'} = $decoration; # set active decoration for callback
my $decoration_label_position = $self->option('decoration_label_position');
return "inside"
if (!$decoration_label_position);
return $decoration_label_position;
}
sub decoration_border {
my $self = shift;
my $decoration = shift;
if (!$decoration)
{
$self->throw("decoration not specified") if (DEBUG);
lib/Bio/Graphics/Glyph/decorated_transcript.pm view on Meta::CPAN
sub draw_component {
my $self = shift;
warn "draw_component(): " . ref($self) . " " . $self->feature . "\n" if (DEBUG == 2);
# draw regular glyph first
if ( $self->feature->source eq 'legend' ) {
# hack, but processed_transcript cannot be drawn without arrow...
$self->Bio::Graphics::Glyph::segments::draw_component(@_);
}
else {
$self->Bio::Graphics::Glyph::processed_transcript::draw_component(@_);
}
# draw decorations if parent information available
if ( $self->{'parent'} and $self->feature->primary_tag eq "CDS") {
return $self->draw_decorations(@_);
}
}
sub draw_decorations {
my $self = shift;
my ( $gd, $dx, $dy ) = @_;
warn "draw_decorations(): " . $self->feature . "\n" if (DEBUG == 2);
my ( $left, $top, $right, $bottom ) = $self->bounds( $dx, $dy );
warn " bounds: left:$left,top:$top,right:$right,bottom:$bottom\n"
if (DEBUG == 2);
foreach my $mh (@{$self->sorted_decorations}) {
# skip invisible decorations
next if ( !$self->decoration_visible($mh) );
# determine overlapping segments between protein decorations and feature components
my $overlap_start_nt = max( $self->feature->start, $mh->start );
my $overlap_end_nt = min( $self->feature->end, $mh->end );
if ( $overlap_start_nt <= $overlap_end_nt ) {
# manual override; forces flip to be drawn flipped
$self->factory->panel->flip( $self->flip )
if ( $self->option('flip_minus') );
my ( $h_left, $h_right ) =
$self->map_no_trunc( $overlap_start_nt, $overlap_end_nt + 1 );
( $h_left, $h_right ) = ( $h_right, $h_left )
if ( $h_left > $h_right );
# my ($h_top, $h_bottom) = ($dy + $self->top + $self->pad_top, $dy + $self->bottom - $self->pad_bottom);
my $h_top = $dy + $self->decoration_top($mh);
my $h_bottom = $dy + $self->decoration_bottom($mh);
my $color = $self->decoration_color($mh);
# don't draw over borders; not supported by SVG
$gd->clip( $left + 1, $h_top, $right - 1, $h_bottom )
if ( !$gd->isa("GD::SVG::Image") );
if ($color ne 'transparent')
{
warn "filledRectangle: left=$h_left,top=$h_top,right=$h_right,bottom=$h_bottom\n"
if (DEBUG == 2);
$gd->filledRectangle( $h_left, $h_top, $h_right, $h_bottom,
$self->factory->translate_color($color) );
}
if ($self->decoration_border($mh))
{
my ($b_left, $b_top, $b_right, $b_bottom) = ($h_left, $h_top, $h_right, $h_bottom);
my $border_color = $self->factory->translate_color($self->decoration_border_color($mh));
warn "border rectangle: left=$b_left,top=$b_top,right=$b_right,bottom=$b_bottom\n"
if (DEBUG == 2);
if ($self->decoration_border($mh) eq "dashed")
{
my $image_class = $self->panel->image_class;
my $gdTransparent = $image_class->gdTransparent;
my $gdStyled = $image_class->gdStyled;
$gd->setStyle($border_color,$border_color,$border_color,$gdTransparent,$gdTransparent);
$gd->rectangle( $b_left, $b_top, $b_right, $b_bottom, $gdStyled );
}
else
{
$gd->rectangle( $b_left, $b_top, $b_right, $b_bottom, $border_color );
}
}
$gd->clip( 0, 0, $gd->width, $gd->height )
if ( !$gd->isa("GD::SVG::Image") );
# draw label on first overlapping component
my $h_label = $self->decoration_label($mh);
if ( $h_label
and (
( $self->feature->strand > 0
and $mh->start >= $self->feature->start )
or ( $self->feature->strand <= 0
and $mh->end <= $self->feature->end )
)
)
{
$self->draw_decoration_label( $gd, $dx, $dy, $mh, $h_top,
$h_left, $h_bottom, $h_right, $h_label );
}
}
}
}
sub draw_decoration_label {
my $self = shift;
my ( $gd, $dx, $dy, $mh, $h_top, $h_left, $h_bottom, $h_right, $label ) = @_;
warn "draw_decoration_label(): " . $self->feature . "\n" if (DEBUG == 2);
my $font = $self->labelfont;
my $label_top = $h_top + ($self->decoration_height($mh)-$font->height)/2;
my $label_pos = $self->decoration_label_position($mh);
lib/Bio/Graphics/Glyph/decorated_transcript.pm view on Meta::CPAN
=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 GFF tag parser should be avoided.
=back
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:
=over
=item * type --> $glyph->active_decoration->type
=item * name --> $glyph->active_decoration->name
=item * nucleotide start coordinate --> $glyph->active_decoration->start
=item * nucleotide end coordinate --> $glyph->active_decoration->end
=item * protein start coordinate --> $glyph->active_decoration->get_tag_values('p_start')
=item * protein end coordinate --> $glyph->active_decoration->get_tag_values('p_end')
=item * score --> $glyph->active_decoration->score
=item * description --> $glyph->active_decoration->description
=back
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).
=head2 OPTIONS
This glyph inherits all options from the L<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.
=head1 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.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::decorated_gene>,
L<Bio::Graphics::Glyph::processed_transcript>
=head1 AUTHOR
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