CIRCOS教程翻译 2.2——karyotype

karyotype核型图，一般的核型图是直线模式，circos将其转换成圆形。karyotype文件格式分两部分，第一部分为染色体的总长和标识，第二部分为每条染色体的基因区域，当然第一部分是必要的。看了一下这一节的内容发现跟第一节的内容有些不一样，看来必须重新写完整的了。

#ideogram.conf
<ideogram>

<spacing>

default = 0.0025r
#break   = 0.5r 同一染色体内部分开的大小，在这一节用不到，怀疑随便找的conf
</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>

#bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 4

#ideogram.position.conf

radius           = 0.90r
thickness        = 75p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

#ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = 0.95r #label的半径直接与圈圈挂钩的，0.95r其实它的位置是在0.95*0.9r位置上
label_size       = 36
label_parallel   = yes
label_case       = lower #英文小写，大写为upper

label_format     = eval(sprintf("chr%s",var(label))) #先格式化label的内容，再进行重写

#ticks.conf
show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label = no
skip_last_label  = no
radius           = dims(ideogram,radius_outer)
tick_separation  = 3p #设定tick最小的范围，也就是说1u这个刻度尺无法显示，另外这个值经过多次测试发现有些问题，暂时还没想清楚，如果想不显示某个刻度，建议直接不写！
multiplier       = 1e-6
color            = black
thickness        = 4p
size             = 20p

<tick>
spacing        = 1u
show_label     = no
thickness      = 2p
color          = dgrey
</tick>

<tick>
spacing        = 5u
show_label     = no
color          = vdgrey
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
</tick>

</ticks>

<<include etc/colors_fonts_patterns.conf>>

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

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

chromosomes_units           = 1000000
chromosomes_display_default = yes #可以不写~~~

karyotype = data/karyotype/karyotype.human.txt #如果有多个物种可以写在一个文件内，不过ID和label不能一样，并且设置不同的颜色加以区分

<<include etc/housekeeping.conf>>