image.png
我们以X染色体为例，来看一下单条染色体circos图画法。
首先看一下整体配置：
<<include colors_fonts_patterns.conf>>
<<include ideogram.conf>>
<<include ticks.conf>>
<image>
<<include etc/image.conf>>
</image>
karyotype = chrX_ karyotype.txt
chromosomes_units = 1000000
chromosomes = hsX
chromosomes_display_default = no
<highlights>
<highlight>
file=highlight.txt.label
r0=0.98r
r1=0.95r
fill_color=blank
z=2
stroke_thickness = 2
</highlight>
</highlights>
<plots>
<plot>
type = scatter
layers_overflow = hide
file = scatter1_blue.bed
r1= 0.88r
r0 = 0.85r
min=0
max=1
extend_bin=no
layers = 4
margin = 0.0200u
thickness = 5
padding = 1
stroke_thickness = 5
stroke_color = dblue
color = dblue
</plot>
<plot>
type = scatter
layers_overflow = hide
file = scatter_red.bed
r1= 0.95r
r0 = 0.9r
min=0
max=2
extend_bin=no
layers = 4
margin = 0.0200u
thickness = 5
padding = 1
stroke_thickness = 5
stroke_color = dred
color = dred
</plot>
<plot>
type = scatter
stroke_thickness = 2
file = snp.txt
fill_color = grey
stroke_color = grey
max = 1
min = 0
r1 = 0.85r
r0 = 0.7r
</plot>
<plot>
type = line
thickness = 5
max_gap = 1u
file = line_red.bed
color = red
fill_color = red
r1 = 0.7r
r0 = 0.6r
</plot>
<plot>
type = line
thickness = 5
max_gap = 1u
file = line_blue.bed
color = blue
fill_color = blue
r1 = 0.5r
r0 = 0.4r
</plot>
<plot>
type = line
thickness = 5
max_gap = 1u
file = red_blue_minus.bed
color = grey
fill_color =grey
r1 = 0.6r
r0 = 0.5r
</plot>
<plot>
type = text
file = label.txt
color = black
r1 = 1.2r
r0 = 1.1r
label_size = 20
label_font = light
padding = 5p
rpadding = 5p
show_links = yes
link_dims = 5p,4p,8p,4p,0p
link_thickness = 2
link_color = dgrey
label_parallel = no
</plot>
</plots>
<<include etc/housekeeping.conf>>
image.png
首先我们看一下核型文件chrX_ karyotype.txt ：
同样的，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 - hsX x 0 155270560 chrx
band hsX p22.33 p22.33 0 4300000 gneg
band hsX p22.32 p22.32 4300000 6000000 gpos50
band hsX p22.31 p22.31 6000000 9500000 gneg
band hsX p22.2 p22.2 9500000 17100000 gpos50
band hsX p22.13 p22.13 17100000 19300000 gneg
band hsX p22.12 p22.12 19300000 21900000 gpos50
band hsX p22.11 p22.11 21900000 24900000 gneg
band hsX p21.3 p21.3 24900000 29300000 gpos100
band hsX p21.2 p21.2 29300000 31500000 gneg
band hsX p21.1 p21.1 31500000 37600000 gpos100
band hsX p11.4 p11.4 37600000 42400000 gneg
band hsX p11.3 p11.3 42400000 46400000 gpos75
band hsX p11.23 p11.23 46400000 49800000 gneg
band hsX p11.22 p11.22 49800000 54800000 gpos25
band hsX p11.21 p11.21 54800000 58100000 gneg
band hsX p11.1 p11.1 58100000 60600000 acen
band hsX q11.1 q11.1 60600000 63000000 acen
band hsX q11.2 q11.2 63000000 64600000 gneg
band hsX q12 q12 64600000 67800000 gpos50
band hsX q13.1 q13.1 67800000 71800000 gneg
band hsX q13.2 q13.2 71800000 73900000 gpos50
band hsX q13.3 q13.3 73900000 76000000 gneg
band hsX q21.1 q21.1 76000000 84600000 gpos100
band hsX q21.2 q21.2 84600000 86200000 gneg
band hsX q21.31 q21.31 86200000 91800000 gpos100
band hsX q21.32 q21.32 91800000 93500000 gneg
band hsX q21.33 q21.33 93500000 98300000 gpos75
band hsX q22.1 q22.1 98300000 102600000 gneg
band hsX q22.2 q22.2 102600000 103700000 gpos50
band hsX q22.3 q22.3 103700000 108700000 gneg
band hsX q23 q23 108700000 116500000 gpos75
band hsX q24 q24 116500000 120900000 gneg
band hsX q25 q25 120900000 128700000 gpos100
band hsX q26.1 q26.1 128700000 130400000 gneg
band hsX q26.2 q26.2 130400000 133600000 gpos25
band hsX q26.3 q26.3 133600000 138000000 gneg
band hsX q27.1 q27.1 138000000 140300000 gpos75
band hsX q27.2 q27.2 140300000 142100000 gneg
band hsX q27.3 q27.3 142100000 147100000 gpos100
band hsX q28 q28 147100000 155270560 gneg
其次我们看一下highlight文件highlight.txt.label：
hsX 0 155270560 chrX
其次就是画散点图了，散点图需要提供位置信息以及y轴坐标，具体示例如下：
hsX 3000000 4000000 1
hsX 4000000 5000000 1
hsX 5000000 6000000 1
hsX 6000000 7000000 1
hsX 7000000 8000000 1
hsX 28000000 29000000 1
hsX 33000000 34000000 1
其次就是线图，同样需要提供坐标信息以及Y轴坐标，具体示例如下：
hsX 10000000 11000000 0.0604048786139
hsX 11000000 12000000 0.0552068874695
hsX 12000000 13000000 0.0380127787297
hsX 13000000 14000000 0.0195789778898
hsX 14000000 15000000 0.0382904053591
hsX 15000000 16000000 0.0724310986976
hsX 16000000 17000000 0.069940660585
hsX 17000000 18000000 0.0570593390352
hsX 18000000 19000000 0.0489131551162
hsX 19000000 20000000 0.0462864194351
hsX 20000000 21000000 0.0651420964831
hsX 21000000 22000000 0.0410705424034
最终效果如下：
image.png
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