image.png
在小华同学那里学得自制circos图核型，图虽小，用处却大，细节易忘，于是不经想动手记录下来。
这个circos图与其他图最大的区别是核型图是自制的
我们先来看一下核型图的写法：
chr - metabolic_process metabolic_process 0 1800 214,0,71
chr - response_to_abiotic_stimulus response_to_abiotic_stimulus 0 1100 0,128,153
chr - response_to_stimulus response_to_stimulus 0 1900 10,71,255
chr - single-organism_cellular_process single-organism_cellular_process 0 1200 238,0,0
chr - single-organism_metabolic_process single-organism_metabolic_process 0 1200 77,187,213
chr - ANAHLS ANAHLS 0 330 0,213,143
chr - CCR2 CCR2 0 330 0,213,143
chr - CYP93D1 CYP93D1 0 330 0,213,143
chr - CYSB CYSB 0 330 0,213,143
chr - DLP DLP 0 330 0,213,143
我们之前说法，核型文件以TAB键分割，前两列可以不变，第三列为染色体实际编号，第四列为图片中显示的编号，第五列代表开始位置，第六列代表终止位置，最后一列实际控制染色体的颜色。
那么根据这个规则，我们可以将第三列改成我们需要展示的内容比如图中的pathway或者基因名称作为“chrom”。其核心的话，是要按照每一个“chrom”设置合适的大小。比如图中基因均设成0-330bp，pathway设成“0-1100”，“0-1800”等等。
其次我们来看下相应的link文件：
同样的也是“染色体编号”，起始位置，终止位置，“染色体编号”，起始位置，终止位置，如下：
Ras_signaling_pathway 0 100 RHS19 0 110
Ras_signaling_pathway 100 200 PGDH 0 66
Ras_signaling_pathway 200 300 TT5 0 110
Ras_signaling_pathway 300 400 SYP121 0 165
Ras_signaling_pathway 400 500 PSP 0 83
Ras_signaling_pathway 500 600 GRF9 0 66
Ras_signaling_pathway 600 700 OPCL1 0 83
Ras_signaling_pathway 700 800 DLP 0 83
Ras_signaling_pathway 800 900 HB 0 110
Ras_signaling_pathway 900 1000 RGP1 0 66
最后让我们来看一下整体配置：
luminance = lum80
<<include colors_fonts_patterns.conf>>
<colors>
a = 0.6
blackweak = 0,0,0,0.75
</colors>
<<include ideogram.conf>>
<<include ticks.conf>>
karyotype = made_karyotype.txt
<image>
<<image.conf>>
</image>
chromosomes_units = 10
<links>
<link>
file = link_1.txt
ribbon = yes
flat = yes # untwist all ribbons
radius = 0.98r
color = chr7_a3
bezier_radius = 0r
stroke_color = vdgrey_a2
stroke_thickness = 2
</link>
<link>
file = link_2.txt
ribbon = yes
flat = yes # untwist all ribbons
radius = 0.98r
color = chr5_a3
bezier_radius = 0r
stroke_color = vdgrey_a4
stroke_thickness = 2
</link>
<link>
file =link_3.txt
ribbon = yes
flat = yes # untwist all ribbons
radius = 0.98r
color = chr12_a2
bezier_radius = 0r
stroke_color = vdgrey_a4
stroke_thickness = 2
</link>
<link>
file = link_4.txt
ribbon = yes
flat = yes # untwist all ribbons
radius = 0.98r
color = chr10_a3
bezier_radius = 0r
stroke_color = vdgrey_a4
stroke_thickness = 2
</link>
<link>
file = link_5.txt
ribbon = yes
flat = yes # untwist all ribbons
radius = 0.98r
color = chr6_a3
bezier_radius = 0r
stroke_color = vdgrey_a4
stroke_thickness = 2
</link>
</links>
<<include /annoroad/share/software/install/circos-0.69/etc/housekeeping.conf>>
data_out_of_range* = trim
