Provided by: libbio-graphics-perl_2.40-2_all 
NAME
Bio::Graphics::Glyph::merged_alignment - The "merged_alignment" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph acts like graded_segments but the bgcolor of segments (sub-feature) is
controlled by binned scores. It also supports semantic zooming to optimize glyph drawing
for larger sequence displays.
OPTIONS
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, the merged-alignment glyph recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------
-max_score Maximum value of the Calculated
feature's "score" attribute
-min_score Minimum value of the Calculated
feature's "score" attribute
-bincolors Colors assigned to bins lightgrey powderblue cornflowerblue blue
(in order)
-bins Bins to which scores are Calculated
assigned
-merge_parts 0 (false)
Whether to simplify the
alignment at low magnification
-max_gap Do not merge across gaps Calculated
that exceed this threshold
If max_score and min_score are not specified, then the glyph will calculate the local
maximum and minimum scores at run time.
If the bins are not specified, they will be calculated based on the number of colors
assigned and the local (or user-specified) minimum and maximum scores. Calculated bins
are equal in size.
User-specified bins are expressed as ranges,
bins = 0-50 50-70 70-90 90-100
where each range means greater than the lower number and less than or equal to the higher
number.
Simplifying the display of alignment features for large segments
The "merge_parts" option is used for semantic zooming. Specifically, if features are
small and dense, they will not be displayed very well for large segments and the color-
coding will be lost. If merge-parts is set to a true value, adjacent alignment parts will
be merged until a gap exceeding a calculated or user-specified value is encountered.
Unless specified, the maximum gap allowed for merging adjacent features is calculated as
(L/10000)*(L/500), where L = the length of the sequence displayed in the browser. The
exponentially increasing gap threshold allows more aggressive merging of alignment
features as the size of the displayed sequence grows larger.
The score of the merged feature is calculated as a weighted average. For example,
consider two adjacent HSPs that are each 400 bp in length and have scores of 60% and 70%.
If the merge_parts option is set to a true value, the two HSPs would be merged in the
display to a single 800 bp alignment block with an average score of 65%.
The merge_parts option is turned off by default.
SAMPLE CONFIGURATION
Sample gbrowse configuration stanzas for an alignment feature using this glyph. The
scores are assumed to be expressed as percent identity (0-100).
# base configuration
[BLASTZ]
feature = blastz_alignment
glyph = merged_alignment
bincolors = #A0A0A0 powderblue cornflowerblue blue
bins = 60-70 70-80 80-90 90-100
category = Sequence Similarity Tracks
height = 6
bump = 1
label = 1
fgcolor = black
key = BLASTZ
Semantic zooming with defined maximum gap between merged features for different zoom
levels
# if the displayed segment is >= 20000 in length,
# use the merge_parts option to simplify the alignment
# display
[BLASTZ:20000]
feature = blastz_alignment
merge_parts = 1
max_gap = 50 # do not merge across gaps > 50 bp
# if the displayed segment is >= 50000 in length
[BLASTZ:50000]
feature = blastz_alignment
merge_parts = 1
max_gap = 500 # do not merge across gaps > 500 bp
--OR--
Semantic zooming with dynamically calculated maximum gap
# if the displayed segment is >= 20000 in length,
[BLASTZ:20000]
feature = blastz_alignment
merge_parts = 1
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI,
Bio::Das, GD
AUTHOR
Sheldon McKay <mckays@cshl.edu>
Copyright (c) 2005 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.