Bio-Graphics

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lib/Bio/Graphics/FeatureFile.pm  view on Meta::CPAN

 	yk53c10.3	15000-15500,15700-15800
 	yk53c10.5	18892-19154

This example is declaring that the ESTs named yk53c10.3 and yk53c10.5
belong to the same group named yk53c10.

=head2 Comments

Lines that begin with the # sign are treated as comments and
ignored. When a # sign appears within a line, everything to the right
of the symbol is also ignored, unless it looks like an HTML fragment or
an HTML color, e.g.:

 # this is ignored
 [Example]
 glyph   = generic   # this comment is ignored
 bgcolor = #FF0000
 link    = http://www.google.com/search?q=$name#results

Be careful, because the processing of # signs uses a regexp heuristic. To be safe, 
always put a space after the # sign to make sure it is treated as a comment.

lib/Bio/Graphics/FeatureFile.pm  view on Meta::CPAN

	return 'config' if $line =~ /^\#/;                               # comment -not a meta
	return 'data';
    }
    return $current_state;
}

sub parse_config_line {
    my $self = shift;
    local $_ = shift;

    # strip right-column comments unless they look like colors or html fragments
    s/\s*\#.*$// unless /\#[0-9a-f]{6,8}\s*$/i || /\w+\#\w+/ || /\w+\"*\s*\#\d+$/;   

    if (/^\s+(.+)/ && $self->{current_tag}) { # configuration continuation line
	my $value = $1;
	my $cc = $self->{current_config} ||= 'general';       # in case no configuration named
	$self->{config}{$cc}{$self->{current_tag}} .= ' ' . $value;
	# respect newlines in code subs
	$self->{config}{$cc}{$self->{current_tag}} .= "\n"
	    if $self->{config}{$cc}{$self->{current_tag}}=~ /^sub\s*\{/;
	return 1;

lib/Bio/Graphics/Glyph/wiggle_box.pm  view on Meta::CPAN

experiments.  Such regions are identified based on raw microarray data but do 
not necessarily have a score associated with them.  In this case, using the 
wiggle_box glyph provides a graphical summary of an expression array experiment.

=head2 DATA

The wiggle data used for this glyph should be loaded using the 'BED' format in
order to allow features of variable width.  The fourth column should be a true
value, with numeric or ".".  An example is shown below:

 track type=wiggle_0 name="transfrags" description="D. melanogaster transcribed fragments 0-2hrs"
 2L      9309    9451    1
 2L      10697   11021   1
 2L      11101   11345   1
 2L      11410   11521   1
 2L      11771   12243   1
 2L      12314   12954   1
 2L      13516   15746   1
 2L      17033   17191   1
 2L      18232   18580   1
 2L      19860   19999   1

lib/Bio/Graphics/Panel.pm  view on Meta::CPAN

You can tile an image onto the panel either before or after it draws
the grid. Simply provide the filename of the image in the -background
or -postgrid options. The image file must be of type PNG, JPEG, XBM or
GIF and have a filename ending in .png, .jpg, .jpeg, .xbm or .gif.

You can also pass a code ref for the -background or -postgrid option,
in which case the subroutine will be invoked at the appropriate time
with the GD::Image object and the Panel object as its two arguments.
You can then use the panel methods to map base pair coordinates into
pixel coordinates and do some custom drawing.  For example, this code
fragment will draw a gray rectangle between bases 500 and 600 to
indicate a "gap" in the sequence:

  my $panel = Bio::Graphics::Panel->new(-segment=>$segment,
                                        -grid=>1,
                                        -width=>600,
                                        -postgrid=> \&draw_gap);
  sub gap_it {
     my $gd    = shift;
     my $panel = shift;
     my ($gap_start,$gap_end) = $panel->location2pixel(500,600);

lib/Bio/Graphics/Panel.pm  view on Meta::CPAN

       $panel->image_and_map(-root => '/var/www/html',
                             -url  => '/tmpimages',
                             -link => 'http://www.google.com/search?q=$name');

   print img({-src=>$url,-usemap=>"#$mapname"});

   print $map;

We call image_and_map() with various arguments (described below) to
generate a three element list consisting of the URL at which the image
can be accessed, an HTML fragment containing the clickable imagemap
data, and the name of the map.  We print out an E<lt>imageE<gt> tag
that uses the URL of the map as its src attribute and the name of the
map as the value of its usemap attribute.  It is important to note
that we must put a "#" in front of the name of the map in order to
indicate that the map can be found in the same document as the
E<lt>imageE<gt> tag.  Lastly, we print out the map itself.

=over 4

=item ($url,$map,$mapname) = $panel-E<gt>image_and_map(@options)