This glyph draws protein sequences. At high magnifications, this
glyph will draw the actual amino acids of the sequence. At low
magnifications, the glyph will plot the Kyte-Doolite hydropathy. By
default, the KD plot will use a window size of 9 residues, but this
can be changed by specifying the kd_window option.
For this glyph to work, the feature must return a protein sequence
string in response to the seq() method.
The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-hilite Highlight color undef (no color)
In addition to the common options, the following glyph-specific
options are recognized:
Option Description Default
------ ----------- -------
-do_kd Whether to draw the Kyte- true
Doolittle hydropathy plot
at low mags
-kd_window Size of the sliding window 9
to use in the KD hydropathy
calculation.
-axis_color Color of the vertical axes fgcolor
in the KD hydropathy plot
None available.
sub draw_component
{ my $self = shift;
my $gd = shift;
my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
my $protein = eval { $self->feature->seq };
$protein = $protein->seq
if ref($protein) and $protein->can('seq');
$protein or return;
$protein = $protein->seq if ref($protein) && $protein->can('seq');
if ($self->dna_fits) {
$self->draw_protein($gd,$protein,$x1,$y1,$x2,$y2);
} elsif ($self->do_kd) {
$self->draw_kd_plot($gd,$protein,$x1,$y1,$x2,$y2);
}} | sub draw_kd_plot
{ my $self = shift;
my $gd = shift;
my $protein = shift;
my ($x1,$y1,$x2,$y2) = @_;
my $kd_window = $self->option('kd_window') || 9;
my %scores = ( I => 4.5,
V => 4.2,
L => 3.8,
F => 2.8,
C => 2.5,
M => 1.9,
A => 1.8,
G => -0.4,
T => -0.7,
W => -0.9,
S => -0.8,
Y => -1.3,
P => -1.6,
H => -3.2,
E => -3.5,
Q => -3.5,
D => -3.5,
N => -3.5,
K => -3.9,
R => -4.5,
);
my @datapoints;
my @seq = split('', uc($protein));
$kd_window = $kd_window < scalar(@seq) ? $kd_window : scalar(@seq);
my $maxkd = 4.5;
my $minkd = -4.5;
my $kd = 0;
for (my $i = 0 ; $i < @seq && $i < $kd_window ; $i++) {
$kd += $scores{$seq[$i]} || 0;
}
my $content = $kd / $kd_window;
push @datapoints, $content;
for (my $i = $kd_window; $i < @seq; $i++) {
$kd -= $scores{$seq[$i-$kd_window]} || 0;
$kd += $scores{$seq[$i]} || 0;
$content = $kd / $kd_window;
push @datapoints, $content;
}
my $scale = $maxkd - $minkd;
foreach (my $i = 0; $i < @datapoints; $i++) {
$datapoints[$i] = ($datapoints[$i] - $minkd) / $scale;
}
my $bin_height = $y2-$y1;
my $fgcolor = $self->fgcolor;
my $bgcolor = $self->factory->translate_color($self->panel->gridcolor);
my $axiscolor = $self->color('axis_color') || $fgcolor;
$gd->line($x1, $y1, $x1, $y2, $axiscolor);
$gd->line($x2-2,$y1, $x2-2,$y2, $axiscolor);
$gd->line($x1, $y1, $x1+3,$y1, $axiscolor);
$gd->line($x1, $y2, $x1+3,$y2, $axiscolor);
$gd->line($x1, ($y2+$y1)/2,$x1+3,($y2+$y1)/2,$axiscolor);
$gd->line($x2-4,$y1, $x2-1, $y1, $axiscolor);
$gd->line($x2-4,$y2, $x2-1, $y2, $axiscolor);
$gd->line($x2-4,($y2+$y1)/2,$x2-1,($y2+$y1)/2,$axiscolor);
$gd->line($x1+5,$y2, $x2-5,$y2, $bgcolor);
$gd->line($x1+5,($y2+$y1)/2,$x2-5,($y2+$y1)/2,$bgcolor);
$gd->line($x1+5,$y1, $x2-5,$y1, $bgcolor);
$gd->string($self->font,$x1+5,$y1,'Kyte-Doolittle hydropathy plot',$axiscolor)
if $bin_height > $self->font->height*2;
$gd->string($self->font,$x2-20,$y1,$maxkd,$axiscolor)
if $bin_height > $self->font->height*2.5;
$gd->string($self->font,$x2-20,$y2-$self->font->height,$minkd,$axiscolor)
if $bin_height > $self->font->height*2.5;
my $graphwidth = $x2 - $x1;
my $scale = $graphwidth / (@datapoints + $kd_window - 1);
for (my $i = 1; $i < @datapoints; $i++) {
my $x = $i + $kd_window / 2;
my $xlo = $x1 + ($x - 1) * $scale;
my $xhi = $x1 + $x * $scale;
my $y = $y2 - ($bin_height*$datapoints[$i]);
$gd->line($xlo, $y2 - ($bin_height*$datapoints[$i-1]),
$xhi, $y,
$fgcolor);
}} | Please report them.