GBrowse之频率直方图，有称为频率分布图，Generating Feature Frequency Histograms，用以展示这些统计信息，可以表意以下信息：
- 不同区段内基因组Gene或者SNP等Feature区间数量分布的差异；
- 基因表达丰度；
- 序列的保守性；
新版的GBrowse更加强了该部分的功能，具体的版本是搞不清楚了，整个过程是GFF2时代使用脚本制备数据，然后再倒入数据库，然后是建立数据库的时候增加–summary参数，增加频率数据的功能，现在时默认就有，在Bio::DB::SeqFeature中，表interval_stats就是专门为支撑统计（summary）的。但这里还是要从GFF2说起，这样有利于弄清楚统计数据的GFF表示，以及如何以普通的feature方式配置进行显示，比如序列的保守性，表达丰度等，需要特殊处理，自己进行统计的生成的数据，就需要用到这个方法。
GFF2时代频率直方图
1、使用 bp_generate_histogram.pl 制备数据，脚本的用法：
Usage: /usr/bin/bp_generate_histogram.pl [options] feature_type1 feature_type2... Dump out a GFF-formatted histogram of the density of the indicated set of feature types. Options: --dsn <dsn> Data source (default dbi:mysql:test) --adaptor <adaptor> Schema adaptor (default dbi::mysqlopt) --user <user> Username for mysql authentication --pass <password> Password for mysql authentication --bin <bp> Bin size in base pairs. --aggregator <list> Comma-separated list of aggregators --sort Sort the resulting list by type and bin --merge Merge features with same method but different sources 例如： bp_generate_histogram.pl -merge -d <> -u <> -p <> -bin 10000 SNP >snp_density.gff
2、注意生成文件的格式：
Chr1 SNP bin 1 10000 49 + . bin Chr1:SNP Chr1 SNP bin 10001 20000 29 + . bin Chr1:SNP 注意，频率数据保存在在第六列
3、数据入库
bp_seqfeature_load.pl -a DBI::mysql -d gb2 snp_density.gff
4、配置GBrowse
[SNP:overview] feature = bin:SNP glyph = xyplot graph_type = boxes scale = right bgcolor = red fgcolor = red height = 20 key = SNP Density
5、OK
参考：http://gmod.org/wiki/GBrowse_Configuration/Feature_frequency_histograms
新版本频率直方图的设置（Summary Mode）
bioperl、GBrowse最新的版本，使用Bio::DB::SeqFeature存储数据。只要在track设置是添加show summary参数。
[TRACK DEFAULTS] ... show summary = 1000000
频率图xyplot的参数说明
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 -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 xyplot 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" attributes -graph_type Type of graph to generate. Histogram Options are: "histogram", "boxes", "line", "points", or "linepoints". -point_symbol Symbol to use. Options are none "triangle", "square", "disc", "filled_triangle", "filled_square", "filled_disc","point", and "none". -point_radius Radius of the symbol, in 4 pixels (does not apply to "point") -scale Position where the Y axis none scale is drawn if any. It should be one of "left", "right", "both" or "none" -graph_height Specify height of the graph Same as the "height" option. -part_color For boxes & points only, none bgcolor of each part (should be a callback). Supersedes -neg_color. -scale_color Color of the scale Same as fgcolor -clip If min_score and/or max_score false are manually specified, then setting this to true will cause values outside the range to be clipped. -bicolor_pivot 0 Where to pivot the two colors when drawing bicolor plots. Scores greater than this value will be drawn using -pos_color. Scores lower than this value will be drawn using -neg_color. -pos_color When drawing bicolor plots, same as bgcolor the fill color to use for values that are above the pivot point. -neg_color When drawing bicolor plots, same as bgcolor the fill color to use for values that are below the pivot point.
参考：
- http://gmod.org/wiki/GBrowse_2.0_HOWTO
- http://search.cpan.org/~lds/Bio-Graphics-2.21/lib/Bio/Graphics/Glyph/xyplot.pm
本文来自：http://boyun.sh.cn/bio/?p=1817