CIRCOS教程翻译 3.1——Wedge Highlights

呵呵，好久没更新了。。。话说这段时间比较忙，自己用之前的三章画了一些circos图深有感触，算是实战了，自我感觉画的还行，但暂时不能放上来，因为还没发表。。。

这一章节是高亮显示数据，显示相应区域的数据或重新定义一个新的ideogram很有用处，结构也比较简单：

#bands.conf
show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 0

#ideogram.position.conf
radius           = 0.85r
thickness        = 50p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

#ideogram.label.conf
show_label       = yes
label_font       = default
label_radius     = dims(ideogram,radius) + 0.15r
label_with_tag   = yes
label_size       = 36
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

#ideogram.conf
<ideogram>
<spacing>
default = 0.01r
break   = 2u
</spacing>
<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>
</ideogram>

#ticks.conf
show_ticks          = yes
show_tick_labels    = yes

show_grid          = yes #网格线的范围
grid_start         = 0.5r
grid_end           = 1.0r

<ticks>
skip_first_label     = no
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 10p
label_separation = 5p
label_offset     = 5p
multiplier       = 1e-6
color            = black

<tick>
spacing        = 1u
size           = 8p
thickness      = 2p
show_label     = no
</tick>
<tick>
spacing        = 5u
size           = 12p
thickness      = 2p
show_label     = yes
label_size     = 20p
format         = %d
grid           = yes
grid_color     = lgrey
grid_thickness = 2p
</tick>
<tick>
spacing        = 10u
size           = 14p
thickness      = 2p
show_label     = yes
label_size     = 24p
format         = %d
grid           = yes #在主刻度上显示网格线
grid_color     = dgrey
grid_thickness = 2p
</tick>
</ticks>

<<include etc/colors_fonts_patterns.conf>>

<<include ideogram.conf>>
<<include ticks.conf>>

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

karyotype   = data/karyotype/karyotype.human.txt

chromosomes_units           = 1000000
chromosomes_display_default = no
chromosomes                 = hs1;hs2;hs3

<highlights>

z          = 0 # z值代表绘图优先级，高的z值将会覆盖低的z值的图像
fill_color = green


<highlight>
file       = data/3/genes.large.txt #格式强制有三列，chr、start、end，后续也可添加其他列
r0         = 0.6r #高亮显示起始位置
r1         = dims(ideogram,radius_inner) #高亮显示终止位置
</highlight>

<highlight>
file       = data/3/genes.large.txt
r0         = 0.7r
r1         = 0.7r + 100p
z          = 5 #覆盖0的图像
fill_color = red
</highlight>

<highlight>
file       = data/3/genes.large.txt
r0         = 0.7r + 100p
r1         = 0.7r + 200p
z          = 10
fill_color = black_a5 #颜色加下划线加a值代表相应的透明度
</highlight>

<highlight>
file         = data/3/genes.large.txt
r0           = 1.075r
r1           = 1.125r
fill_color   = blue
stroke_color = vdblue
stroke_thickness = 2
</highlight>

<highlight>
file         = data/3/genes.large.txt
r0           = 1.09r
r1           = 1.11r
fill_color   = orange
z            = 5
</highlight>

</highlights>

<<include etc/housekeeping.conf>>