CIRCOS教程翻译 1.6——axe和background

最新推荐文章于 2024-09-27 15:55:25 发布

翻译最新推荐文章于 2024-09-27 15:55:25 发布 · 3.1k 阅读

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本文详细介绍了基因组可视化配置的各项参数设置，包括不同颜色的染色体表示、背景区域的划分、链接文件的设定等，并展示了如何通过配置文件实现丰富的可视化效果。

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axe和background属于坐标轴，前者是细线条，后者是宽线条- -！！！能这样翻译么- -！！！按照字面意思来讲，background是背景的意思，说那么多还不如画出来实在，例子添加了两个conf，但为了大家能看明白，将其写在主配置文件内比较容易理解，当然也可以多写个conf，使主配置文件简洁一些：

karyotype = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000

chromosomes_display_default = no
chromosomes                 = /hs[1234]$/

<colors>
chr1* = red
chr2* = orange
chr3* = green
chr4* = blue
</colors>

chromosomes_reverse = /hs[234]/
chromosomes_scale   = hs1=0.5r,/hs[234]/=0.5rn

<plots>

<plot>

type = histogram
file = data/5/segdup.hs1234.hist.txt
r1   = 0.88r
r0   = 0.81r

fill_color = vdgrey
extend_bin = no

<rules>
<<include exclude.hs1.rule>> #将排除hs1的脚本另写一个conf
</rules>

<backgrounds> #使用y0和y1进行设定范围
show  = data
<background>
color = vvlgrey #最内一层
</background>
<background>
color = vlgrey
y0    = 0.2r
y1    = 0.5r
</background>
<background>
color = lgrey
y0    = 0.5r
y1    = 0.8r 
</background>
<background>
color = grey #最外面一层
y0    = 0.8r 
</background>
</backgrounds>
#当然你也可以用这个：<<include backgrounds.conf>>

</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.stacked.txt
r1   = 0.99r
r0   = 0.92r

fill_color  = hs1,hs2,hs3,hs4
orientation = in
extend_bin  = no

<rules>
<<include exclude.hs1.rule>>
</rules>

<axes> #spacing控制线条的间距，而position控制具体的线条
show = data
thickness = 1
color     = lgrey
<axis>
spacing   = 0.1r #默认间距0.1r为lgrey，宽度为1
</axis>
<axis>
spacing   = 0.2r #每0.2r的间距为grey
color     = grey
</axis>
<axis>
position  = 0.5r #在0.5r时线为red
color     = red
</axis>
<axis>
position  = 0.85r #在0.85r时线为green
color     = green
thickness = 2
</axis>
</axes>
#同样的：<<include axes.conf>>

</plot>

</plots>

<links>

<link>
file          = data/5/segdup.txt
radius        = 0.8r
bezier_radius = 0r
color         = black_a4
thickness     = 2

<rules>
<rule>
condition     = var(intrachr)
show          = no
</rule>
<rule>
condition     = 1
color         = eval(var(chr2))
flow          = continue
</rule>
<rule>
condition     = from(hs1)
radius1       = 0.99r
</rule>
<rule>
condition     = to(hs1)
radius2       = 0.99r
</rule>

</rules>

</link>

</links>

<<include ideogram.conf>>

<<include ticks.conf>>

<image>
<<include etc/image.conf>>                
</image>

<<include etc/colors_fonts_patterns.conf>> 

<<include etc/housekeeping.conf>>