NAME
Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
SYNOPSIS
# This script parses a GenBank or EMBL file named on the command
# line and produces a PNG rendering of it. Call it like this:
# render.pl my_file.embl | display -
use strict;
use Bio::Graphics;
use Bio::SeqIO;
my $file = shift or die "provide a sequence file as the argument";
my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
my $seq = $io->next_seq or die "could not find a sequence in the file";
my @features = $seq->all_SeqFeatures;
# sort features by their primary tags
my %sorted_features;
for my $f (@features) {
my $tag = $f->primary_tag;
push @{$sorted_features{$tag}},$f;
}
my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => 'between',
-width => 800,
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track( arrow => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-bump => 0,
-double=>1,
-tick => 2);
$panel->add_track(generic => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-glyph => 'generic',
-bgcolor => 'blue',
-label => 1,
);
# general case
my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
my $idx = 0;
for my $tag (sort keys %sorted_features) {
my $features = $sorted_features{$tag};
$panel->add_track($features,
-glyph => 'generic',
-bgcolor => $colors[$idx++ % @colors],
-fgcolor => 'black',
-font2color => 'red',
-key => "${tag}s",
-bump => +1,
-height => 8,
-label => 1,
-description => 1,
);
}
print $panel->png;
$panel->finished;
exit 0;DESCRIPTION
The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, physical (contig) maps, or any other type of map in which a set of discrete ranges need to be laid out on the number line.
The module supports a drawing style in which each type of feature occupies a discrete "track" that spans the width of the display. Each track will have its own distinctive "glyph", a configurable graphical representation of the feature.
The module also supports a more flexible style in which several different feature types and their associated glyphs can occupy the same track. The choice of glyph is under run-time control.
Semantic zooming (for instance, changing the type of glyph depending on the density of features) is supported by a callback system for configuration variables. The module has built-in support for Bio::Das stylesheets, and stylesheet-driven configuration can be intermixed with semantic zooming, if desired.
You can add a key to the generated image using either of two key styles. One style places the key captions at the top of each track. The other style generates a graphical key at the bottom of the image.
Note that this module depends on GD. The optional SVG output depends on GD::SVG and SVG.
METHODS
This section describes the class and object methods for Bio::Graphics::Panel.
Typically you will begin by creating a new Bio::Graphics::Panel object, passing it the desired width of the image to generate and an origin and length describing the coordinate range to display. The Bio::Graphics::Panel->new() method has may configuration variables that allow you to control the appearance of the image.
You will then call add_track() one or more times to add sets of related features to the picture. add_track() places a new horizontal track on the image, and is likewise highly configurable. When you have added all the features you desire, you may call png() to convert the image into a PNG-format image, or boxes() to return coordinate information that can be used to create an imagemap.
CONSTRUCTORS
new() is the constructor for Bio::Graphics::Panel:
- $panel = Bio::Graphics::Panel->new(@options)
-
The new() method creates a new panel object. The options are a set of tag/value pairs as follows:
Option Value Default ------ ----- ------- -offset Base pair to place at extreme left none of image, in zero-based coordinates -length Length of sequence segment, in bp none -start Start of range, in 1-based none coordinates. -stop Stop of range, in 1-based none coordinates. -end Same as -stop. -segment A Bio::SeqI or Das::Segment none object, used to derive sequence range if not otherwise specified. -width Desired width of image, in pixels 600 -spacing Spacing between tracks, in pixels 5 -pad_top Additional whitespace between top 0 of image and contents, in pixels -pad_bottom Additional whitespace between top 0 of image and bottom, in pixels -pad_left Additional whitespace between left 0 of image and contents, in pixels -pad_right Additional whitespace between right 0 of image and bottom, in pixels -bgcolor Background color for the panel as a white whole -key_color Background color for the key printed wheat at bottom of panel (if any) -key_spacing Spacing between key glyphs in the 10 key printed at bottom of panel (if any) -key_font Font to use in printed key gdMediumBoldFont captions. -key_style Whether to print key at bottom of none panel ("bottom"), between each track ("between"), to the left of each track ("left"), to the right of each track ("right") or not at all ("none"). -add_category_labels false Whether to add the "category" to the track key. The category is an optional argument that can be attached to each track. If a category is present, and this option is true, then the category will be added to the track label in parentheses. For example, if -key is "Protein matches" and -category is "vertebrate", then the track will be labeled "Protein matches (vertebrate)". -auto_pad If "left" or "right" keys are in use true then setting auto_pad to a true value will allow the panel to adjust its width in order to accomodate the length of the longest key. -empty_tracks What to do when a track is empty. suppress Options are to suppress the track completely ("suppress"), to show just the key in "between" mode ("key"), to draw a thin grey line ("line"), or to draw a dashed line ("dashed"). -flip flip the drawing coordinates left false to right, so that lower coordinates are to the right. This can be useful for drawing (-) strand features. -all_callbacks Whether to invoke callbacks on false the automatic "track" and "group" glyphs. -grid Whether to draw a vertical grid in false the background. Pass a scalar true value to have a grid drawn at regular intervals (corresponding to the minor ticks of the arrow glyph). Pass an array reference to draw the grid at the specified positions. -gridcolor Color of the grid lightcyan -extend_grid If true, extend the grid into the pad false top and pad_bottom regions -background An image or callback to use for the none background of the image. Will be invoked I<before> drawing the grid. -postgrid An image or callback to use for the none background of the image. Will be invoked I<after> drawing the grid. -truecolor Create a truecolor (24-bit) image. false Useful when working with the "image" glyph. -image_class To create output in scalable vector graphics (SVG), optionally pass the image class parameter 'GD::SVG'. Defaults to using vanilla GD. See the corresponding image_class() method below for details. -link, -title, -target These options are used when creating imagemaps for display on the web. See L</"Creating Imagemaps">.Typically you will pass new() an object that implements the Bio::RangeI interface, providing a length() method, from which the panel will derive its scale.
$panel = Bio::Graphics::Panel->new(-segment => $sequence, -width => 800);new() will return undef in case of an error.
Note that if you use the "left" or "right" key styles, you are responsible for allocating sufficient -pad_left or -pad_right room for the labels to appear. The necessary width is the number of characters in the longest key times the font width (gdMediumBoldFont by default) plus 3 pixels of internal padding. The simplest way to calculate this is to iterate over the possible track labels, find the largest one, and then to compute its width using the formula:
$width = gdMediumBoldFont->width * length($longest_key) +3;In order to obtain scalable vector graphics (SVG) output, you should pass new() the -image_class=>'GD::SVG' parameter. This will cause Bio::Graphics::Panel to load the optional GD::SVG module. See the gd() and svg() methods below for additional information.
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); my $top = $panel->top; my $bottom = $panel->bottom; my $gray = $panel->translate_color('gray'); $gd->filledRectangle($gap_start,$top,$gap_end,$bottom,$gray); }
OBJECT METHODS
- $track = $panel->add_track($glyph,$features,@options)
-
The add_track() method adds a new track to the image.
Tracks are horizontal bands which span the entire width of the panel. Each track contains a number of graphical elements called "glyphs", corresponding to a sequence feature.
There are a large number of glyph types. By default, each track will be homogeneous on a single glyph type, but you can mix several glyph types on the same track by providing a code reference to the -glyph argument. Other options passed to add_track() control the color and size of the glyphs, whether they are allowed to overlap, and other formatting attributes. The height of a track is determined from its contents and cannot be directly influenced.
The first two arguments are the glyph name and an array reference containing the list of features to display. The order of the arguments is irrelevant, allowing either of these idioms:
$panel->add_track(arrow => \@features); $panel->add_track(\@features => 'arrow');The glyph name indicates how each feature is to be rendered. A variety of glyphs are available, and the number is growing. You may omit the glyph name entirely by providing a -glyph argument among @options, as described below.
Currently, the following glyphs are available:
Name Description ---- ----------- anchored_arrow a span with vertical bases |---------|. If one or the other end of the feature is off-screen, the base will be replaced by an arrow. arrow An arrow; can be unidirectional or bidirectional. It is also capable of displaying a scale with major and minor tickmarks, and can be oriented horizontally or vertically. cds Draws CDS features, using the phase information to show the reading frame usage. At high magnifications draws the protein translation. crossbox A box with a big "X" inside it. diamond A diamond, useful for point features like SNPs. dna At high magnification draws the DNA sequence. At low magnifications draws the GC content. dot A circle, useful for point features like SNPs, stop codons, or promoter elements. ellipse An oval. extending_arrow Similar to arrow, but a dotted line indicates when the feature extends beyond the end of the canvas. generic A filled rectangle, nondirectional. graded_segments Similar to segments, but the intensity of the color is proportional to the score of the feature. This is used for showing the intensity of blast hits or other alignment features. group A group of related features connected by a dashed line. This is used internally by Panel. image A pixmap image that will be layered on top of the graphic. heterogeneous_segments Like segments, but you can use the source field of the feature to change the color of each segment. line A simple line. pinsertion A triangle designed to look like an insertion location (e.g. a transposon insertion). processed_transcript multi-purpose representation of a spliced mRNA, including positions of UTRs primers Two inward pointing arrows connected by a line. Used for STSs. redgreen_box A box that changes from green->yellow->red as the score of the feature increases from 0.0 to 1.0. Useful for representing microarray results. rndrect A round-cornered rectangle. segments A set of filled rectangles connected by solid lines. Used for interrupted features, such as gapped alignments. ruler_arrow An arrow with major and minor tick marks and interval labels. toomany Tries to show many features as a cloud. Not very successful. track A group of related features not connected by a line. This is used internally by Panel. transcript Similar to segments, but the connecting line is a "hat" shape, and the direction of transcription is indicated by a small arrow. transcript2 Similar to transcript, but the direction of transcription is indicated by a terminal exon in the shape of an arrow. translation 1, 2 and 3-frame translations. At low magnifications, can be configured to show start and stop codon locations. At high magnifications, shows the multi-frame protein translation. triangle A triangle whose width and orientation can be altered. xyplot Histograms and other graphs plotted against the genome. whiskerplot Box and whisker plot for statistical dataIf the glyph name is omitted from add_track(), the "generic" glyph will be used by default. To get more information about a glyph, run perldoc on "Bio::Graphics::Glyph::glyphname", replacing "glyphname" with the name of the glyph you are interested in.
The @options array is a list of name/value pairs that control the attributes of the track. Some options are interpretered directly by the track. Others are passed down to the individual glyphs (see "GLYPH OPTIONS"). The following options are track-specific:
Option Description Default ------ ----------- ------- -tkcolor Track color white -glyph Glyph class to use. "generic" -stylesheet Bio::Das::Stylesheet to none use to generate glyph classes and options.-tkcolor controls the background color of the track as a whole.
-glyph controls the glyph type. If present, it supersedes the glyph name given in the first or second argument to add_track(). The value of -glyph may be a constant string, a hash reference, or a code reference. In the case of a constant string, that string will be used as the class name for all generated glyphs. If a hash reference is passed, then the feature's primary_tag() will be used as the key to the hash, and the value, if any, used to generate the glyph type. If a code reference is passed, then this callback will be passed each feature in turn as its single argument. The callback is expected to examine the feature and return a glyph name as its single result.
Example:
$panel->add_track(\@exons, -glyph => sub { my $feature = shift; $feature->source_tag eq 'curated' ? 'ellipse' : 'generic'; } );The -stylesheet argument is used to pass a Bio::Das stylesheet object to the panel. This stylesheet will be called to determine both the glyph and the glyph options. If both a stylesheet and direct options are provided, the latter take precedence.
If successful, add_track() returns an Bio::Graphics::Glyph object. You can use this object to add additional features or to control the appearance of the track with greater detail, or just ignore it. Tracks are added in order from the top of the image to the bottom. To add tracks to the top of the image, use unshift_track().
Adding groups of features: It is not uncommon to add a group of features which are logically connected, such as the 5' and 3' ends of EST reads. To group features into sets that remain on the same horizontal position and bump together, pass the sets as an anonymous array. For example:
$panel->add_track(segments => [[$abc_5,$abc_3], [$xxx_5,$xxx_3], [$yyy_5,$yyy_3]] );Typical usage is:
$panel->add_track( transcript => \@genes, -fillcolor => 'green', -fgcolor => 'black', -bump => +1, -height => 10, -label => 1); - $track = unshift_track($glyph,$features,@options)
-
unshift_track() works like add_track(), except that the new track is added to the top of the image rather than the bottom.
- $track = $panel->insert_track($position,$glyph,$features,@options)
-
This works like add_track(), but the track is inserted into the indicated position. The track will be inserted before the indicated position; thus specify a track of 0 to insert the new track at the beginning.
- $gd = $panel->gd([$gd])
-
The gd() method lays out the image and returns a GD::Image object containing it. You may then call the GD::Image object's png() or jpeg() methods to get the image data.
Optionally, you may pass gd() a preexisting GD::Image object that you wish to draw on top of. If you do so, you should call the width() and height() methods first to ensure that the image has sufficient dimensions.
If you passed new() the -image_class=>'GD::SVG' parameter, the gd() method returns a GD::SVG::Image object. This object overrides GD::Image methods in order to generate SVG output. It behaves exactly as described for GD::Image objects with one exception: it implements and svg() method instead of the png() or jpeg() methods. Currently there is no direct access to underlying SVG calls but this is subject to change in the future.
- $png = $panel->png
-
The png() method returns the image as a PNG-format drawing, without the intermediate step of returning a GD::Image object.
- $svg = $panel->svg
-
The svg() method returns the image in an XML-ified SVG format.
- $panel->finished
-
Bio::Graphics creates memory cycles. When you are finished with the panel, you should call its finished() method. Otherwise you will have memory leaks. This is only an issue if you're going to create several panels in a single program.
- $image_class = $panel->image_class
-
The image_class() method returns the current drawing package being used, currently one of GD or GD::SVG. This is primarily used internally to ensure that calls to GD's exported methods are called in an object-oriented manner to avoid compile time undefined string errors. This is usually not needed for external use.
- $image_package = $panel->image_package
-
This accessor method, like image_class() above is provided as a convenience. It returns the current image package in use, currently one of GD::Image or GD::SVG::Image. This is not normally used externally.
- $polygon_package = $panel->polygon_package
-
This accessor method, like image_package() above is provided as a convenience. It returns the current polygon package in use, currently one of GD::Polygon or GD::SVG::Polygon. This is not normally used externally except in the design of glyphs.
- $boxes = $panel->boxes
- @boxes = $panel->boxes
-
The boxes() method returns a list of arrayrefs containing the coordinates of each glyph. The method is useful for constructing an image map. In a scalar context, boxes() returns an arrayref. In an list context, the method returns the list directly.
Each member of the list is an arrayref of the following format:
[ $feature, $x1, $y1, $x2, $y2, $track ]The first element is the feature object; either an Ace::Sequence::Feature, a Das::Segment::Feature, or another Bioperl Bio::SeqFeatureI object. The coordinates are the topleft and bottomright corners of the glyph, including any space allocated for labels. The track is the Bio::Graphics::Glyph object corresponding to the track that the feature is rendered inside.
- $boxes = $panel->key_boxes
- @boxes = $panel->key_boxes
-
Returns the positions of the track keys as an arrayref or a list, depending on context. Each value in the list is an arrayref of format:
[ $key_text, $x1, $y1, $x2, $y2, $track ] - $position = $panel->track_position($track)
-
After calling gd() or boxes(), you can learn the resulting Y coordinate of a track by calling track_position() with the value returned by add_track() or unshift_track(). This will return undef if called before gd() or boxes() or with an invalid track.
- @pixel_coords = $panel->location2pixel(@feature_coords)
-
Public routine to map feature coordinates (in base pairs) into pixel coordinates relative to the left-hand edge of the picture. If you define a -background callback, the callback may wish to invoke this routine in order to translate base coordinates into pixel coordinates.
- $left = $panel->left
- $right = $panel->right
- $top = $panel->top
- $bottom = $panel->bottom
-
Return the pixel coordinates of the drawing area of the panel, that is, exclusive of the padding.
GLYPH OPTIONS
Each glyph has its own specialized subset of options, but some are shared by all glyphs:
Option Description Default
------ ----------- -------
-key Description of track for undef
display in the track label.
-category The category of the track undef
for display in the
track label.
-fgcolor Foreground color black
-bgcolor Background color turquoise
-linewidth Width of lines drawn by 1
glyph
-height Height of glyph 10
-font Glyph font gdSmallFont
-fontcolor Primary font color black
-font2color Secondary font color turquoise
-label Whether to draw a label false
-description Whether to draw a false
description
-bump Bump direction 0
-sort_order Specify layout sort order "default"
-bump_limit Maximum number of levels undef (unlimited)
to bump
-hbumppad Additional horizontal 0
padding between bumped
features
-strand_arrow Whether to indicate undef (false)
strandedness
-stranded Synonym for -strand_arrow undef (false)
-part_labels Whether to label individual undef (false)
subparts.
-part_label_merge Whether to merge undef (false)
adjacent subparts when
labeling.
-connector Type of connector to none
use to connect related
features. Options are
"solid," "hat", "dashed",
"quill" and "none".
-all_callbacks Whether to invoke undef
callbacks for autogenerated
"track" and "group" glyphs
-subpart_callbacks Whether to invoke false
callbacks for subparts of
the glyph.
-box_subparts Return boxes around feature false
subparts rather than around the
feature itself.
-link, -title, -target
These options are used when creating imagemaps
for display on the web. See L</"Creating Imagemaps">.Specifying colors: Colors can be expressed in either of two ways: as symbolic names such as "cyan" and as HTML-style #RRGGBB triples. The symbolic names are the 140 colors defined in the Netscape/Internet Explorer color cube, and can be retrieved using the Bio::Graphics::Panel->color_names() method.
Foreground color: The -fgcolor option controls the foreground color, including the edges of boxes and the like.
Background color: The -bgcolor option controls the background used for filled boxes and other "solid" glyphs. The foreground color controls the color of lines and strings. The -tkcolor argument controls the background color of the entire track.
Track color: The -tkcolor option used to specify the background of the entire track.
Font color: The -fontcolor option controls the color of primary text, such as labels
Secondary Font color: The -font2color option controls the color of secondary text, such as descriptions.
Labels: The -label argument controls whether or not the ID of the feature should be printed next to the feature. It is accepted by all glyphs. By default, the label is printed just above the glyph and left aligned with it.
-label can be a constant string or a code reference. Values can be any of:
-label value Description
------------ -----------
0 Don't draw a label
1 Calculate a label based on primary tag of sequence
"a string" Use "a string" as the label
code ref Invoke the code reference to compute the labelA known bug with this naming scheme is that you can't label a feature with the string "1". To work around this, use "1 " (note the terminal space).
Descriptions: The -description argument controls whether or not a brief description of the feature should be printed next to it. By default, the description is printed just below the glyph and left-aligned with it. A value of 0 will suppress the description. A value of 1 will "magically" look for tags of type "note" or "description" and draw them if found, otherwise the source tag, if any, will be displayed. A code reference will be invoked to calculate the description on the fly. Anything else will be treated as a string and used verbatim.
Connectors: A glyph can contain subglyphs, recursively. The top level glyph is the track, which contains one or more groups, which contain features, which contain subfeatures, and so forth. By default, the "group" glyph draws dotted lines between each of its subglyphs, the "segment" glyph draws a solid line between each of its subglyphs, and the "transcript" and "transcript2" glyphs draw hat-shaped lines between their subglyphs. All other glyphs do not connect their components. You can override this behavior by providing a -connector option, to explicitly set the type of connector. Valid options are:
"hat" an upward-angling conector
"solid" a straight horizontal connector
"quill" a decorated line with small arrows indicating strandedness
(like the UCSC Genome Browser uses)
"dashed" a horizontal dashed line.The -connector_color option controls the color of the connector, if any.
Collision control: The -bump argument controls what happens when glyphs collide. By default, they will simply overlap (value 0). A -bump value of +1 will cause overlapping glyphs to bump downwards until there is room for them. A -bump value of -1 will cause overlapping glyphs to bump upwards. You may also provide a -bump value of +2 or -2 to activate a very simple type of collision control in which each feature occupies its own line. This is useful for showing dense, nearly-full length features such as similarity hits. The bump argument can also be a code reference; see below.
If you would like to see more horizontal whitespace between features that occupy the same line, you can specify it with the -hbumppad option. Positive values increase the amount of whitespace between features. Negative values decrease the whitespace.
Keys: The -key argument declares that the track is to be shown in a key appended to the bottom of the image. The key contains a picture of a glyph and a label describing what the glyph means. The label is specified in the argument to -key.
box_subparts: Ordinarily, when you invoke the boxes() methods to retrieve the rectangles surrounding the glyphs (which you need to do to create clickable imagemaps, for example), the rectangles will surround the top level features. If you wish for the rectangles to surround subpieces of the glyph, such as the exons in a transcript, set box_subparts to a true numeric value. The value you specify will control the number of levels of subfeatures that the boxes will descend into. For example, if using the "gene" glyph, set -box_subparts to 2 to create boxes for the whole gene (level 0), the mRNAs (level 1) and the exons (level 2).
part_labels: If set to true, each subpart of a multipart feature will be labeled with a number starting with 1 at the 5'-most part. This is useful for counting exons. You can pass a callback to this argument; the part number and the total number of parts will be arguments three and four. For example, to label the exons as "exon 1", "exon 2" and so on:
-part_labels => sub {
my ($feature,undef,$partno) = @_;
return 'exon '.($partno+1);
}The -label argument must also be true.
part_labels_merge: If true, changes the behavior of -part_labels so that features that abut each other without a gap are treated as a single feature. Useful if you want to count the UTR and CDS segments of an exon as a single unit, and the default for transcript glyphs.
strand_arrow: If set to true, some glyphs will indicate their strandedness, usually by drawing an arrow. For this to work, the Bio::SeqFeature must have a strand of +1 or -1. The glyph will ignore this directive if the underlying feature has a strand of zero or undef.
sort_order: By default, features are drawn with a layout based only on the position of the feature, assuring a maximal "packing" of the glyphs when bumped. In some cases, however, it makes sense to display the glyphs sorted by score or some other comparison, e.g. such that more "important" features are nearer the top of the display, stacked above less important features. The -sort_order option allows a few different built-in values for changing the default sort order (which is by "left" position): "low_score" (or "high_score") will cause features to be sorted from lowest to highest score (or vice versa). "left" (or "default") and "right" values will cause features to be sorted by their position in the sequence. "longest" (or "shortest") will cause the longest (or shortest) features to be sorted first, and "strand" will cause the features to be sorted by strand: "+1" (forward) then "0" (unknown, or NA) then "-1" (reverse).
In all cases, the "left" position will be used to break any ties. To break ties using another field, options may be strung together using a "|" character; e.g. "strand|low_score|right" would cause the features to be sorted first by strand, then score (lowest to highest), then by "right" position in the sequence.
Finally, a subroutine coderef with a $$ prototype can be provided. It will receive two glyph as arguments and should return -1, 0 or 1 (see Perl's sort() function for more information). For example, to sort a set of database search hits by bits (stored in the features' "score" fields), scaled by the log of the alignment length (with "start" position breaking any ties):
sort_order = sub ($$) {
my ($glyph1,$glyph2) = @_;
my $a = $glyph1->feature;
my $b = $glyph2->feature;
( $b->score/log($b->length)
<=>
$a->score/log($a->length) )
||
( $a->start <=> $b->start )
}It is important to remember to use the $$ prototype as shown in the example. Otherwise Bio::Graphics will quit with an exception. The arguments are subclasses of Bio::Graphics::Glyph, not the features themselves. While glyphs implement some, but not all, of the feature methods, to be safe call the two glyphs' feature() methods in order to convert them into the actual features.
The '-always_sort' option, if true, will sort features even if bumping is turned off. This is useful if you would like overlapping features to stack in a particular order. Features towards the end of the list will overlay those towards the beginning of the sort order.
bump_limit: When bumping is chosen, colliding features will ordinarily move upward or downward without limit. When many features collide, this can lead to excessively high images. You can limit the number of levels that features will bump by providing a numeric bump_limit option.
Options and Callbacks
Instead of providing a constant value to an option, you may subsitute a code reference. This code reference will be called every time the panel needs to configure a glyph. The callback will be called with three arguments like this:
sub callback {
my ($feature,$option_name,$part_no,$total_parts,$glyph) = @_;
# do something which results in $option_value being set
return $option_value;
}The five arguments are $feature, a reference to the IO::SeqFeatureI object, $option_name, the name of the option to configure, $part_no, an integer index indicating which subpart of the feature is being drawn, $total_parts, an integer indicating the total number of subfeatures in the feature, and finally $glyph, the Glyph object itself. The latter fields are useful in the case of treating the first or last subfeature differently, such as using a different color for the terminal exon of a gene. Usually you will only need to examine the first argument. This example shows a callback examining the score() attribute of a feature (possibly a BLAST hit) and return the color "red" for high-scoring features, and "green" for low-scoring features:
sub callback {
my $feature = shift;
if ($feature->score > 90) {
return 'red';
else {
return 'green';
}
}The callback should return a string indicating the desired value of the option. To tell the panel to use the default value for this option, return the string "*default*".
When you install a callback for a feature that contains subparts, the callback will be invoked first for the top-level feature, and then for each of its subparts (recursively). You should make sure to examine the feature's type to determine whether the option is appropriate.
Some glyphs deliberately disable this recursive feature. The "track", "group", "transcript", "transcript2" and "segments" glyphs selectively disable the -bump, -label and -description options. This is to avoid, for example, a label being attached to each exon in a transcript, or the various segments of a gapped alignment bumping each other. You can override this behavior and force your callback to be invoked by providing add_track() with a true -all_callbacks argument. In this case, you must be prepared to handle configuring options for the "group" and "track" glyphs.
In particular, this means that in order to control the -bump option with a callback, you should specify -all_callbacks=>1, and turn on bumping when the callback is in the track or group glyphs.
The -subpart_callbacks options is similar, except that when this is set to true callbacks are invoked for the main glyph and its subparts. This option only affects the -label and -description options.
ACCESSORS
The following accessor methods provide access to various attributes of the panel object. Called with no arguments, they each return the current value of the attribute. Called with a single argument, they set the attribute and return its previous value.
Note that in most cases you must change attributes prior to invoking gd(), png() or boxes(). These three methods all invoke an internal layout() method which places the tracks and the glyphs within them, and then caches the result.
Accessor Name Description
------------- -----------
width() Get/set width of panel
spacing() Get/set spacing between tracks
key_spacing() Get/set spacing between keys
length() Get/set length of segment (bp)
flip() Get/set coordinate flipping
pad_top() Get/set top padding
pad_left() Get/set left padding
pad_bottom() Get/set bottom padding
pad_right() Get/set right padding
start() Get the start of the sequence (bp; read only)
end() Get the end of the sequence (bp; read only)
left() Get the left side of the drawing area (pixels; read only)
right() Get the right side of the drawing area (pixels; read only)COLOR METHODS
The following methods are used internally, but may be useful for those implementing new glyph types.
- @names = Bio::Graphics::Panel->color_names
-
Return the symbolic names of the colors recognized by the panel object. In a scalar context, returns an array reference.
- ($red,$green,$blue) = Bio::Graphics::Panel->color_name_to_rgb($color)
-
Given a symbolic color name, returns the red, green, blue components of the color. In a scalar context, returns an array reference to the rgb triplet. Returns undef for an invalid color name.
- @rgb = $panel->rgb($index)
-
Given a GD color index (between 0 and 140), returns the RGB triplet corresponding to this index. This method is only useful within a glyph's draw() routine, after the panel has allocated a GD::Image and is populating it.
- $index = $panel->translate_color($color)
-
Given a color, returns the GD::Image index. The color may be symbolic, such as "turquoise", or a #RRGGBB triple, as in #F0E0A8. This method is only useful within a glyph's draw() routine, after the panel has allocated a GD::Image and is populating it.
- $panel->set_pen($width,$color)
-
Changes the width and color of the GD drawing pen to the values indicated. This is called automatically by the GlyphFactory fgcolor() method. It returns the GD value gdBrushed, which should be used for drawing.
Creating Imagemaps
You may wish to use Bio::Graphics to create clickable imagemaps for display on the web. The main method for achieving this is image_and_map(). Under special circumstances you may instead wish to call either or both of create_web_image() and create_web_map().
Here is a synopsis of how to use image_and_map() in a CGI script, using CGI.pm calls to provide the HTML scaffolding:
print h2('My Genome');
my ($url,$map,$mapname) =
$panel->image_and_map(-root => '/var/www/html',
-url => '/tmpimages',
-link => 'http://www.google.com/search?q=$name');
print img({-src=>$url,-usemap=>"#$mapname"});
print $map;We call image_and_map() with various arguments (described below) to generate a three element list consisting of the URL at which the image can be accessed, an HTML fragment containing the clickable imagemap data, and the name of the map. We print out an <image> tag that uses the URL of the map as its src attribute and the name of the map as the value of its usemap attribute. It is important to note that we must put a "#" in front of the name of the map in order to indicate that the map can be found in the same document as the <image> tag. Lastly, we print out the map itself.
- ($url,$map,$mapname) = $panel->image_and_map(@options)
-
Create the image in a web-accessible directory and return its URL, its clickable imagemap, and the name of the imagemap. The following options are recognized:
Option Description ------ ----------- -url The URL to store the image at. -root The directory path that should be appended to the start of -url in order to obtain a physical directory path. -link A string pattern or coderef that will be used to generate the outgoing hypertext links for the imagemap. -title A string pattern or coderef that will be used to generate the "title" tags of each element in the imagemap (these appear as popup hint boxes in certain browsers). -target A string pattern or coderef that will be used to generate the window target for each element. This can be used to pop up a new window when the user clicks on an element. -mapname The name to use for the E<lt>mapE<gt> tag. If not provided, a unique one will be autogenerated for you.This method returns a three element list consisting of the URL at which the image has been written to, the imagemap HTML, and the name of the map. Usually you will incorporate this information into an HTML document like so:
my ($url,$map,$mapname) = $panel->image_and_map(-link=>'http://www.google.com/searche?q=$name'); print qq(<img src="$url" usemap="#$map">),"\n"; print $map,"\n"; - $url = $panel->create_web_image($url,$root)
-
Create the image, write it into the directory indicated by concatenating $root and $url (i.e. "$root/$url"), and return $url.
- $map = $panel->create_web_map('mapname',$linkrule,$titlerule,$targetrule)
-
Create a clickable imagemap named "mapname" using the indicated rules to generate the hypertext links, the element titles, and the window targets for the graphical elements. Return the HTML for the map, including the enclosing <map> tag itself.
To use this method effectively, you will need a web server and an image directory in the document tree that is writable by the web server user. For example, if your web server's document root is located at /var/www/html, you might want to create a directory named "tmpimages" for this purpose:
mkdir /var/www/html/tmpimages
chmod 1777 /var/www/html/tmpimagesThe 1777 privilege will allow anyone to create files and subdirectories in this directory, but only the owner of the file will be able to delete it.
When you call image_and_map(), you must provide it with two vital pieces of information: the URL of the image directory and the physical location of the web server's document tree. In our example, you would call:
$panel->image_and_map(-root => '/var/www/html',-url=>'/tmpimages');If you are working with virtual hosts, you might wish to provide the hostname:portnumber part of the URL. This will work just as well:
$panel->image_and_map(-root => '/var/www/html',
-url => 'http://myhost.com:8080/tmpimages');If you do not provide the -root argument, the method will try to figure it out from the DOCUMENT_ROOT environment variable. If you do not provide the -url argument, the method will assume "/tmp".
During execution, the image_and_map() method will generate a unique name for the image using the Digest::MD5 module. You can get this module on CPAN and it must be installed in order to use image_and_map(). The imagename will be a long hexadecimal string such as "e7457643f12d413f20843d4030c197c6.png". Its URL will be /tmpimages/e7457643f12d413f20843d4030c197c6.png, and its physical path will be /var/www/html/tmpimages/e7457643f12d413f20843d4030c197c6.png
In addition to providing directory information, you must also tell image_and_map() how to create outgoing links for each graphical feature, and, optionally, how to create the "hover title" (the popup yellow box displayed by most modern browsers), and the name of the window or frame to link to when the user clicks on it.
There are three ways to specify the link destination:
By configuring one or more tracks with a -link argument.
By configuring the panel with a -link argument.
By passing a -link argument in the call to image_and_map().
The -link argument can be either a string or a coderef. If you pass a string, it will be interpreted as a URL pattern containing runtime variables. These variables begin with a dollar sign ($), and are replaced at run time with the information relating to the selected annotation. Recognized variables include:
$name The feature's name (display name)
$id The feature's id (eg, PK from a database)
$class The feature's class (group class)
$method The feature's method (same as primary tag)
$source The feature's source
$ref The name of the sequence segment (chromosome, contig)
on which this feature is located
$description The feature's description (notes)
$start The start position of this feature, relative to $ref
$end The end position of this feature, relative to $ref
$segstart The left end of $ref displayed in the detailed view
$segend The right end of $ref displayed in the detailed viewFor example, to link each feature to a Google search on the feature's description, use the argument:
-link => 'http://www.google.com/search?q=$description'Be sure to use single quotes around the pattern, or Perl will attempt to perform variable interpretation before image_and_map() has a chance to work on it.
You may also pass a code reference to -link, in which case the code will be called every time a URL needs to be generated for the imagemap. The subroutine will be called with two arguments, the feature and the Bio::Graphics::Panel object, and it should return the URL to link to, or an empty string if a link is not desired. Here is a simple example:
-link => sub {
my ($feature,$panel) = @_;
my $type = $feature->primary_tag;
my $name = $feature->display_name;
if ($primary_tag eq 'clone') {
return "http://www.google.com/search?q=$name";
} else {
return "http://www.yahoo.com/search?p=$name";
}The -link argument cascades. image_and_map() will first look for a -link option in the track configuration, and if that's not found, it will look in the Panel configuration (created during Bio::Graphics::Panel->new). If no -link configuration option is found in either location, then image_and_map() will use the value of -link passed in its argument list, if any.
The -title and -target options behave in a similar manner to -link. -title is used to assign each feature "title" and "alt" attributes. The "title" attribute is used by many browsers to create a popup hints box when the mouse hovers over the feature's glyph for a preset length of time, while the "alt" attribute is used to create navigable menu items for the visually impaired. As with -link, you can set the title by passing either a substitution pattern or a code ref, and the -title option can be set in the track, the panel, or the method call itself in that order of priority.
If not provided, image_and_map() will autogenerate its own title in the form "<method> <display_name> <seqid>:start..end".
The -target option can be used to specify the window or frame that clicked features will link to. By default, when the user clicks on a feature, the loaded URL will replace the current page. You can modify this by providing -target with the name of a preexisting or new window name in order to create effects like popup windows, multiple frames, popunders and the like. The value of -target follows the same rules as -title and -link, including variable substitution and the use of code refs.
NOTE: Each time you call image_and_map() it will generate a new image file. Images that are identical to an earlier one will reuse the same name, but those that are different, even by one pixel, will result in the generation of a new image. If you have limited disk space, you might wish to check the images directory periodically and remove those that have not been accessed recently. The following cron script will remove image files that haven't been accessed in more than 20 days.
30 2 * * * find /var/www/html/tmpimages -type f -atime +20 -exec rm {} \;
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::redgreen_box, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::xyplot, Bio::Graphics::Glyph::whiskerplot, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD GD::SVG
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.