【可视化】circos之一爱的魔力转圈圈

image.png

有没有那么一个圈，就这么吸引住了你的眼球.....
有没有那么一个圆，就这么抓住了你的心.....

从最初第一眼看到circos就被其美貌捕获,最近正好用的频率有点高，不禁想稍稍整理一下。

circos图最核心的也是最巧妙以及最复杂的就是其它的配置文件了circos.conf。
一般的circos.conf 首先需要引入ideogram.conf (核型设置) ticks.conf (ticks的设置)等等，其次绘制染色体核型，主要是在图片上显示染色体，其次是plot部分以及link部分。

image.png

格式如下：

<<include colors_fonts_patterns.conf>>
<<include ideogram.conf>>
<<include ticks.conf>>
<image>
<<include etc/image.conf>>
</image>


karyotype   = karyotype.human.hg19.txt
chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4;hs5;hs6;hs7;hs8;hs9;hs10;hs11;hs12;hs13;hs14;hs15;hs16;hs17;hs18;hs19;hs20;hs21;hs22;hsX;hsY
chromosomes_display_default = no


<plots>
<plot>
#.......
</plot>
</plots>


<links>
<link>
#........
</link>
</links>
<<include etc/housekeeping.conf>>

那么我们首先来看核型如下：
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。

chr - hs1 1 0 249250621 chr1
chr - hs2 2 0 243199373 chr2
chr - hs3 3 0 198022430 chr3
chr - hs4 4 0 191154276 chr4
chr - hs5 5 0 180915260 chr5
chr - hs6 6 0 171115067 chr6
chr - hs7 7 0 159138663 chr7
chr - hs8 8 0 146364022 chr8
chr - hs9 9 0 141213431 chr9
chr - hs10 10 0 135534747 chr10
chr - hs11 11 0 135006516 chr11
chr - hs12 12 0 133851895 chr12
chr - hs13 13 0 115169878 chr13
chr - hs14 14 0 107349540 chr14
chr - hs15 15 0 102531392 chr15
chr - hs16 16 0 90354753 chr16
chr - hs17 17 0 81195210 chr17
chr - hs18 18 0 78077248 chr18
chr - hs19 19 0 59128983 chr19
chr - hs20 20 0 63025520 chr20
chr - hs21 21 0 48129895 chr21
chr - hs22 22 0 51304566 chr22
chr - hsX x 0 155270560 chrx
chr - hsY y 0 59373566 chry
band hs1 p36.33 p36.33 0 2300000 gneg
band hs1 p36.32 p36.32 2300000 5400000 gpos25

plot 部分可以画散点图，直方图等等。而这里我们只用来标记基因列表。也就是用到它的text部分.

text文件格式如下：
文件依然以TAB分割，前三列为染色体起始终止位置，最后一列为基因名称也就是标签信息

hs10    51606988        51607988        TIMM23
hs10    51732772        51733772        PARGP1
hs17    20904276        20905276        USP22
hs14    50053331        50054331        RN7SL1
hs1     32053130        32054130        TINAGL1
hs14    50329493        50330493        RN7SL2
hs20    32078107        32079107        CBFA2T2
hs10    105152223       105153223       USMG5
hs4     6698890 6699890 S100P
hs6     62284046        62285046        MTRNR2L9
hs17    7571954 7572954 TP53
hs14    50053372        50054372        RN7SL1
hs7     20193816        20194816        MACC1
hs16    11642638        11643638        LITAF
hs14    50053372        50054372        RN7SL1

之后我们来看一下 text的配置：

<plots>
<plot>
type  = text
file =label_example.txt
color = black
r1    = 1.6r
r0    = 1.1r
label_size = 40
label_font = light
padding    = 5p
rpadding   = 5p

label_snuggle = yes
max_snuggle_distance = 2r
snuggle_sampling = 2
snuggle_tolerance = 0.25r
snuggle_link_overlap_tolerance = 2p

show_links     = yes
link_dims      = 5p,4p,8p,4p,0p
link_thickness = 2
link_color     = dgrey
label_parallel   = no
</plot>
</plots>

处理完了text，我们再把链接加上，也就是link部分:
link 文件如下：
link也是以TAB分割，分别代表弧线左端的位置和右端的位置。

hs17    20904276        20904276        hs14    50053331        50053331
hs1     32053130        32053130        hs14    50329493        50329493
hs20    32078107        32078107        hs10    105152223       105152223
hs4     6698890 6698890 hs6     62284046        62284046
hs17    7571954 7571954 hs14    50053372        50053372
hs16    11642638        11642638        hs14    50053372        50053372
hs4     77080773        77080773        hs14    50053332        50053332
hs11    18264199        18264199        hs14    50053372        50053372
hs14    50053354        50053354        hsX     70520319        70520319

看一下link配置：

<links>
<link>
file =  links.txt
radius        = 0.98r
bezier_radius = 0r
color         = 204,171,187
thickness     = 8
<rules>
<rule>
condition     = 1
color = "black"
#color         = eval(var(chr2))
flow          = continue
</rule>
</rules>
</link>
</links>

最终效果如下：

image.png

整体配置如下:

<<include colors_fonts_patterns.conf>>
<<include ideogram.conf>>
<<include ticks.conf>>
<image>
<<include etc/image.conf>>
</image>
karyotype   = karyotype.human.hg19.txt

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4;hs5;hs6;hs7;hs8;hs9;hs10;hs11;hs12;hs13;hs14;hs15;hs16;hs17;hs18;hs19;hs20;hs21;hs22;hsX;hsY
chromosomes_display_default = no
<plots>
<plot>
type  = text
file =text_example.txt
color = black
r1    = 1.6r
r0    = 1.1r
label_size = 40
label_font = light
padding    = 5p
rpadding   = 5p

label_snuggle = yes
max_snuggle_distance = 2r
snuggle_sampling = 2
snuggle_tolerance = 0.25r
snuggle_link_overlap_tolerance = 2p

show_links     = yes
link_dims      = 5p,4p,8p,4p,0p
link_thickness = 2
link_color     = dgrey
label_parallel   = no
</plot>
</plots>
<links>
<link>
file =  links.txt
radius        = 0.98r
bezier_radius = 0r
color         = 204,171,187
thickness     = 8
<rules>
<rule>
condition     = 1
color = "black"
#color         = eval(var(chr2))
flow          = continue
</rule>
</rules>
</link>
</links>
<<include etc/housekeeping.conf>>