gbrowse图形显示配置

Gbrowse图谱可以分为三部分,overview,region,details,每一部分都可以显示0到多个的映描(track),对于trace的定义,可以分为以下几部分:

  • * track显示的内容,显示什么样的数据
  • * track显示为什么样子,具体的样式
  • * track有关的文字描述
  • * track有关的行为,比如冒泡提示,点击或者经过时的行为,启动的链接

更为复杂的主题包括:

  • * 显示样式、内容的动态话
  • * 多种来源、多种类型的数据组合
  • * 不同缩放比例,显示不同的样式
  • * 对于显示数据内容数目的限制
  • * track的层级分类,一个track下可以分为多个不同的下级track
  • * 密度图、频率图显示
  • * 不同用户的权限管理

图示

GBrowse截图及其标注

配置示例

[Density:overview]在overview区域显示
feature       = density feature的类型,可以是多个,也可以使用来源进行限制
glyph         = xyplot Track显示的图形样式
graph_type    = boxes  下面都是选择xyplot后,设定的相应的参数
max_score     = 60
min_score     = 0
scale         = none
bgcolor       = red
fgcolor       = red
height        = 20
label         = 0 每一feature是否显示标题
key           = Density histograms /10k 该Track的标题

[GC:region] 在Region取显示
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
gc_window    = auto
strand       = both
fgcolor      = red
axis_color   = blue
key          = DNA/GC Content

[Genes] 在details区显示
feature      = gene
glyph        = so_transcript
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
label        = sub { my $f = shift;
                     my $name = $f->display_name;
                     my @aliases = $f->attributes('Alias');
                     $name .= " (@aliases)" if @aliases;
             $name;
  } 
height       = 6
description  = 0
key          = Named gene

[mRNA]
feature      = exon
glyph        = transcript
description  = 1
height       = 10
sixframe     = 1
label        = sub {shift->name . " reading frame"}
key          = mRNA

[CDS]
feature      = CDS
glyph        = transcript2
height       = 10
connector    = 1
connector_color =black
strand_arrow =1
key          = CDS

[tRNAs]
feature       = tRNA
glyph         = generic
bgcolor       = lightgray
fgcolor       = black
height        = 4
stranded      = 1
description   = 1
key           = tRNAs

[rRNA]
feature       = rRNA
fgcolor       = orange
glyph         = generic
description   = 1
key           = rRNAs

[pseudogene]
feature       = pseudogene
glyph        = gene
bgcolor       = lightgray
fgcolor       = black
height        = 4
key           = pseudogene

[pseudogenic region]
feature       = pseudogenic_region
glyph         = segments
bgcolor       = lightgray
fgcolor       = black
height        = 4
key           = pseudogenic region
description   = 0

[mobile element]
feature       = mobile_element
glyph         = segments
bgcolor       = lightgray
fgcolor       = black
height        = 4
description   = 0
key           = mobile element

[processed transcript]
feature       = processed_transcript
glyph         = generic
bgcolor       = lightgray
fgcolor       = black
height        = 4
description   = 0
key           = processed transcript

glyph支持的类型

glyph指定的类型,实际上画图调用的是 Bio::Graphics相应的方法,而具体画图可以设定的变量以及相应的意义,也可以通过查看 Bio::Graphics 模块的文档获得。支持的类型包括:

Bio::Graphics::Glyph::Factory
Bio::Graphics::Glyph::alignment
Bio::Graphics::Glyph::anchored_arrow 锚
Bio::Graphics::Glyph::arrow
Bio::Graphics::Glyph::box
Bio::Graphics::Glyph::broken_line
Bio::Graphics::Glyph::cds
Bio::Graphics::Glyph::christmas_arrow
Bio::Graphics::Glyph::crossbox
Bio::Graphics::Glyph::dashed_line 虚线
Bio::Graphics::Glyph::diamond 菱形
Bio::Graphics::Glyph::dna
Bio::Graphics::Glyph::dot 点
Bio::Graphics::Glyph::dumbbell 哑铃
Bio::Graphics::Glyph::ellipse 椭圆
Bio::Graphics::Glyph::ex
Bio::Graphics::Glyph::extending_arrow
Bio::Graphics::Glyph::flag 旗帜
Bio::Graphics::Glyph::gene
Bio::Graphics::Glyph::generic
Bio::Graphics::Glyph::graded_segments 精细的
Bio::Graphics::Glyph::group
Bio::Graphics::Glyph::heterogeneous_segments 混杂的
Bio::Graphics::Glyph::image
Bio::Graphics::Glyph::lightning 闪电
Bio::Graphics::Glyph::line
Bio::Graphics::Glyph::merge_parts 合并
Bio::Graphics::Glyph::merged_alignment
Bio::Graphics::Glyph::minmax
Bio::Graphics::Glyph::oval 椭圆
Bio::Graphics::Glyph::pentagram 五角星
Bio::Graphics::Glyph::pinsertion
Bio::Graphics::Glyph::primers
Bio::Graphics::Glyph::processed_transcript
Bio::Graphics::Glyph::protein
Bio::Graphics::Glyph::ragged_ends 凹凸不平的
Bio::Graphics::Glyph::redgreen_box
Bio::Graphics::Glyph::redgreen_segment
Bio::Graphics::Glyph::repeating_shape
Bio::Graphics::Glyph::rndrect
Bio::Graphics::Glyph::ruler_arrow
Bio::Graphics::Glyph::saw_teeth
Bio::Graphics::Glyph::segmented_keyglyph
Bio::Graphics::Glyph::segments
Bio::Graphics::Glyph::so_transcript
Bio::Graphics::Glyph::span
Bio::Graphics::Glyph::splice_site
Bio::Graphics::Glyph::stackedplot 堆积线
Bio::Graphics::Glyph::ternary_plot 三重曲线
Bio::Graphics::Glyph::text_in_box
Bio::Graphics::Glyph::three_letters 三个字母
Bio::Graphics::Glyph::tic_tac_toe
Bio::Graphics::Glyph::toomany
Bio::Graphics::Glyph::track
Bio::Graphics::Glyph::transcript
Bio::Graphics::Glyph::transcript2
Bio::Graphics::Glyph::translation
Bio::Graphics::Glyph::triangle 三角形
Bio::Graphics::Glyph::two_bolts
Bio::Graphics::Glyph::wave 波浪
Bio::Graphics::Glyph::weighted_arrow
Bio::Graphics::Glyph::whiskerplot 细微的曲线
Bio::Graphics::Glyph::xyplot

图形的收集与展示

只有想不到的,没有做不到的,后面会收集与展示GBrowse丰富的track展示截图。

SNP展示使用GBrowse展示SNP数据

频率图GBrowse频率图示例

转录组数据展示GBrowse展示转录丰度数据

比较基因组
GBrowse展示比较基因组数据

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 » 转载文章请注明,转载自:博耘生物 » 《gbrowse图形显示配置》
 » 原文链接:http://boyun.sh.cn/bio/?p=1798

2 thoughts on “gbrowse图形显示配置

  1. Pingback: gbrowse图形显示配置 | Public Library of Bioinformatics

  2. 您好,看到该博文受益匪浅!!
    然后想问一下,该页的最后一张Gbrowse的图(比较基因组的)是如何画的呢?不知道能否提示一下,感谢!!

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