/
TUTORIAL
190 lines (149 loc) · 12.4 KB
/
TUTORIAL
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
link:images/example_labels.png
= Bio::Graphics tutorial
Copyright (C) 2007, 2008 Jan Aerts <jan.aerts@gmail.com>
License: The Ruby License
Homepage: http://bio-graphics.rubyforge.org
(If you'd like to know how the code itself works, please see the README.DEV)
== Overview and terms used
This Bio::Graphics library allows for drawing overviews of genomic regions, similar to the pictures drawn by gbrowse[http://www.gmod.org/wiki/index.php/Gbrowse]. Basically, it allows creating simple images that display features on a linear map, including the position of subdomains in a protein (see picture). It's now also possible to create vertical pictures.
link:images/protein_domains.png
link:images/vertical.png
Any Bio::Graphics image consists of the following parts (concepts and nomenclature identical to that from bioperl[http://www.bioperl.org/wiki/Main_Page]):
* one panel: container of all tracks
* one or more tracks: container of the features. Multiple tracks can exist in the same graphic to allow for differential visualization of different feature types (e.g. genes as blue rectangles and polymorphisms as red triangles)
* one or more features in each track: these are the actual features that you want to display (e.g. 'gene 1', 'SNP 123445')
* a ruler on top of the panel: is added automatically
Schematically:
panel
+-> track 1
| +-> feature 1
| +-> feature 2
| +-> feature 3
+-> track 2
| +-> feature 4
| +-> feature 5
+-> ruler
Below is an annotated version of the picture at the top of the page. The whole picture makes up the panel, which contains one ruler and 3 tracks ('scaffolds', 'markers' and 'clones'). Each of these tracks has zero or more features.
link:images/terms.png
== Glyphs
According to Wikipedia, a _glyph_ is "the shape given in a particular typeface to a specific grapheme or symbol". In the context of Bio::Graphics, a glyph is just the thing that represents one single feature. Several kinds of glyph exist to allow for features that are on a particular strand as well as for spliced features. See the picture below for an overview.
link:images/glyph_showcase.png
If the view is really zoomed out, arrow on the directed glyphs are not shown, as they would be bigger than the glyph itself.
== Use
The code below was used to create the picture showing all the different glyphs mentioned above. This is not the nicest piece of code, but it is the simplest. It is straightforward to parse a GFF file and create a picture based on that. See my blog[http://saaientist.blogspot.com/2007/09/graphics-genomics-and-ruby.html] for an nicer example.
For an explanation of the arguments with each method for this example, see the Bio::Graphics::Panel and Bio::Graphics::Track object documentation.
1 # Load the library
2 require 'bio-graphics' # or require_gem 'bio-graphics' or gem 'bio-graphics'
3
4 # Create the panel
5 my_panel = Bio::Graphics::Panel.new(500, :width => 1000)
6
7 # Create the tracks
8 generic_track = my_panel.add_track('generic', :label => false)
9 line_track = my_panel.add_track('line', :label => false, :glyph => :line, :colour => [0,0,1])
10 line_with_handles_track = my_panel.add_track('line_with_handles', :label => false, :glyph => :line_with_handles, [1,0,0])
11 directed_track = my_panel.add_track('directed', :label => false, :glyph => :directed_generic, :colour => [0,1,0])
12 triangle_track = my_panel.add_track('triangle', :label => false, :glyph => :triangle, :colour => [1,0,0])
13 spliced_track = my_panel.add_track('spliced', :label => false, :glyph => :spliced, :colour => [1,0,0])
14 directed_spliced_track = my_panel.add_track('directed_spliced', :label => false, :glyph => :directed_spliced, :colour => [1,0,1])
15 composite_track = my_panel.add_track('composite_features', :label => false, :glyph => { 'utr' => :line, 'cds' => :directed_spliced})
16
17 # Add features to each track
18 generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :link => 'http://www.newsforge.com')
19 generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :link => 'http://www.thearkdb.org')
20 generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :link => 'http://www.google.com')
21
22 line_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
23 line_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
24
25 line_with_handles_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
26 line_with_handles_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
27
28 directed_track.add_feature(Bio::Feature.new('primer', '50..60'), :link => 'http://www.google.com')
29 directed_track.add_feature(Bio::Feature.new('primer', 'complement(80..120)'), :link => 'http://www.sourceforge.net')
30
31 triangle_track.add_feature(Bio::Feature.new('snp', '56'))
32 triangle_track.add_feature(Bio::Feature.new('snp', '103'), :link => 'http://digg.com')
33
34 spliced_track.add_feature(Bio::Feature.new('spliced', 'join(34..52,109..183)'), :link => 'http://news.bbc.co.uk')
35 spliced_track.add_feature(Bio::Feature.new('spliced', 'complement(join(170..231,264..299,350..360,409..445))'))
36 spliced_track.add_feature(Bio::Feature.new('spliced', 'join(134..152,209..283)'))
37
38 directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(34..52,109..183)'), :link => 'http://www.vrtnieuws.net')
39 directed_spliced_track.add_feature(Bio::Feature.new('cds', 'complement(join(170..231,264..299,350..360,409..445))'), :link => 'http://bioinformatics.roslin.ac.uk')
40 directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(134..152,209..283)'))
41
42 utr5 = Bio::Feature.new('utr', '100..150')
43 cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
44 utr3 = Bio::Feature.new('utr', '330..375')
45
46 transcript = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [utr5,cds,utr3])
47 composite_track.add_feature(transcript, :label => 'my_transcript')
48
49 # Draw the thing
50 my_panel.draw('glyph_showcase.png')
Let's walk through this:
* Line 2: load the actual library code. Make sure that the library is in your RUBYLIB path.
* Line 5: Create the panel, which is nothing more than the canvas you'll be working on. The following parameters were used:
* The sequence is 500 bp long.
* The width of the picture will be 1000 points.
* Lines 8-15: Create the different tracks. Parameters are:
* name.
* flag if feature labels should be drawn (here: false)
* the default glyph for features in this track. This can be overridden on a feature-by-feature basis. See the picture above and Bio::Graphics::Track#new for allowed values.
* the default colour for features in this track. This can also be overridden on a feature-by-feature basis. At the moment in RGB. (This will probably change to colour names in the future).
* Lines 18-47: Add features to each track. Parameters are:
* a Bio::Feature object. (See bioruby documentation at http://www.bioruby.org)
* the label to be used
* link.
* Line 50: Create the actual picture. If the the initial Panel#new call contains the parameter ":clickable => true" (in line 5), a HTML file is created as well.
That's pretty clear, but what's happening with the composite_track (on lines 15 and 42-47)?
To set the glyph for a feature (or the default glyph in a track), you normally use a symbol, like :generic or :directed_spliced. For composite features, however, we've made it possible to have different subfeatures drawn in different ways. In this example: we want to draw the UTRs as thin lines, while the CDS is big boxes connected with thin lines.
How does this work? See lines 42 to 47. If the feature you're adding to a track has subfeatures, you can use the type of the subfeature to direct the glyph to use. In the example above: the utr5 and utr3 have 'utr' as the first argument in the Bio::Feature#new, and the cds object has 'cds'. The transcript that gets created in line 46 takes these three Bio::Feature objects as subfeatures (the last argument). Now up in line 15 we set the glyph of this track to the hash {'utr' => :line, 'cds' => :directed_spliced}. What this does, is it takes each subfeature in turn, and draws it using the glyph that matches its type.
=== Hyperlinks
There are no graphic formats that are inherently clickable (SVG is a special case and the _display_ of it is not the SVG itself). Therefore, in case the user wants a clickable graphic, an accompanying HTML file is created with the same name as the picture but obviously the .html extension. This file contains the map and will display a clickable picture when loaded in a webbrowser.
=== Custom glyphs
The user can easily create custom glyphs to add to the functionality of the Bio::Graphics library. The only thing that has to be done is add a file to lib/bio/graphics/glyphs. The file should look like this:
module Bio::Graphics::Glyph
class Bio::Graphics::Glyph::SomeName < Bio::Graphics::Glyph::Common
def draw
@feature_context.rectangle(x1, y1, x2, y2).fill
end
end
end
What are the properties of that file?
* It's name has to be the same as the class name specified on the second line, but in snake_case instead of CamelCase. The above file therefore should be called some_name.rb.
* Give the class a sensible name (in CamelCase).
* Just define the draw method. Have a look at the other files in the glyphs/ directory for examples. Some values you can use:
* Bio::Graphics::FEATURE_HEIGHT = default height in pixels for a glyph
* Bio::Graphics::FEATURE_ARROW_LENGTH = default width in pixels of arrows on features
=== Setting options dynamically
In some circumstances, you might want to have the colour of a feature depend on some characteristic of the feature itself. A prime example is the score of a BLAST hit: the higher the score, the more 'red' the bar should be; the lower the score, the more 'pink'. This is easily achievable: instead of just setting the default feature colour within a track to a fixed colour (e.g. [0,1,0]), use a lambda function.
An example. Suppose we want to show a bunch of features that should be red if they're longer than 1000 bp and green if they're shorter than 1000 bp. The following code will do that:
generic_track = my_panel.add_track('generic', :label => false,
:colour => lambda do |feature|
if (feature.stop - feature.start) > 1000
return [1,0,0] # i.e. 'red'
else
return [0,1,0] # i.e. 'green's
end
)
== Download and installation
As of May 2008, development of the library has moved from rubyforge to github at http://github.com/jandot/bio-graphics. I've moved away from SVN and embraced git as the new source control system.
There are different ways to install the library.
* The easiest way: gem install bio-graphics (although this will get you the last version on rubyforge which will probably not be updated)
* The other way: "git clone git://github.com/jandot/bio-graphics.git" or use the download button at http://github.com/jandot/bio-graphics
== Prerequisites
You'll need to have the following installed to use this library:
* bioruby (http://www.bioruby.org), to parse the feature locations.
* cairo (http://cairographics.org), to do the actual drawing.
* pango (http://www.pango.org), to do the high level text drawing.
=== Ubuntu
* gem install bio
* sudo apt-get install libcairo-ruby
=== Windows (thanks to Naohisa Goto)
Install Ruby-GNOME2 Win32 GUI Installer, which contains rcairo-1.2.6. Get it from ruby-gnome2.sourceforge.jp/?News_20070212_1 (ruby-gnome2-0.16.0-1-i386-mswin32.exe)
During installation, check the "Register enviroment variables" option.
=== Mac OSX (thanks to Ed Allen and _why)
I've been successful in installing Bio::Graphics on a Mac by meticulously following the steps from http://code.whytheluckystiff.net/shoes/wiki/BuildingShoesOnOsx. After that, I got the ruby-bindings for pango by installing ruby-gnome2 from http://ruby-gnome2.sourceforge.jp. Unfortunately, the compilation step returns an error, complaining about a file rbpangolayoutiter.c. Changing line 22 in that file to "#if 0" solves this problem.
YMMV.