Circos是使用Perl写的程序，主要通过输入配置文件来作图。
- 安装
conda install circos
- 安装好后，检查依赖的模块是否安装好
circos -modules
image.png
若安装有问题请移步：https://www.dazhuanlan.com/2020/02/10/5e40c06de4f85/
- 查看帮助
circos -man #q退出
- 使用 （举个小栗子）
准备数据文件：
mitogenome.txt
chr - Cerasus_campanulata Cerasus_campanulata 1 434334 chr1
chr - Eriobotrya_japonica Eriobotrya_japonica 1 434980 chr2
chr - Fragaria_orientalis Fragaria_orientalis 1 275143 chr3
chr - Malus_domestica Malus_domestica 1 396947 chr4
chr - Malus_domestica_cultivar_Yantai_fuji_8 Malus_domestica_cultivar_Yantai_fuji_8 1 396947 chr5
chr - Malus_hupehensis_var.mengshanensis Malus_hupehensis_var.mengshanensis 1 422555 chr6
chr - Malus_x_domestica_cultivar_Golden_delicious Malus_x_domestica_cultivar_Golden_delicious 1 396947 chr7
chr - Prunus_avium Prunus_avium 1 444567 chr8
chr - Pyrus_betulifolia Pyrus_betulifolia 1 469928 chr9
chr - Rosa_chinensis Rosa_chinensis 1 313448 chr10
chr - Rosa_sp.JP-2020 Rosa_sp.JP-2020 1 303484 chr11
chr - Sorbus_aucuparia Sorbus_aucuparia 1 384977 chr12
chr - Sorbus_torminalis Sorbus_torminalis 1 386758 chr13
第四列是最终图中染色体的名字，第五列是染色体的起始位置，第六列是终止位置，最后一列是对应染色体的颜色（circos配置好的）
links.txt
Cerasus_campanulata 361313 361366 Eriobotrya_japonica 165335 165388
Cerasus_campanulata 361679 371694 Eriobotrya_japonica 125924 138060
Cerasus_campanulata 372750 378588 Eriobotrya_japonica 381870 388067
Cerasus_campanulata 382877 383111 Eriobotrya_japonica 389595 389824
Cerasus_campanulata 383295 388281 Eriobotrya_japonica 42226 47124
Cerasus_campanulata 388922 389054 Eriobotrya_japonica 27833 27957
Cerasus_campanulata 389399 391598 Eriobotrya_japonica 104435 106674
Cerasus_campanulata 399111 399770 Eriobotrya_japonica 328684 329261
Cerasus_campanulata 401795 401855 Eriobotrya_japonica 116778 116838
Cerasus_campanulata 402607 403615 Eriobotrya_japonica 367945 368916
Cerasus_campanulata 403769 407869 Eriobotrya_japonica 282620 286544
Cerasus_campanulata 407904 408066 Eriobotrya_japonica 289586 289730
Cerasus_campanulata 408195 408444 Eriobotrya_japonica 294047 294301
Cerasus_campanulata 408662 409100 Eriobotrya_japonica 356944 357381
Cerasus_campanulata 409209 411330 Eriobotrya_japonica 239141 241361
Cerasus_campanulata 412248 416430 Eriobotrya_japonica 304340 308555
Cerasus_campanulata 424008 424801 Eriobotrya_japonica 242674 243457
Cerasus_campanulata 426379 426826 Eriobotrya_japonica 87515 87992
- 配置文件
ideogram.conf
<ideogram>
show = yes
<spacing>
default = 5u
# The " " are required because
# the trailing /> is interpreted as a block end.
# Otherwise, you can also use a space
# <pairwise /hs/ /hs/ >
<pairwise "/hs/ /hs/">
spacing = 0.001r
</pairwise>
</spacing>
thickness = 30p
#stroke_thickness = 0
#stroke_color = dgrey
fill = yes
fill_color = black
radius = 0.80r
show_label = yes
label_font = default
label_radius = dims(ideogram,radius_outer) + 250p
label_size = 24p
label_parallel = yes
show_bands = yes
fill_bands = yes
band_stroke_thickness = 0
band_stroke_color = black
band_transparency = 4
</ideogram>
links.conf
<links>
#################################################
<link>
# 指定link文件路径，其数据格式为：
# chr1 start1 end1 chr2 start2 end2
file = data/karyotype/links.txt
# 设置links曲线的半径
radius = 0.31r
# 设置贝塞尔曲线半径，该值越大越扁平，不好看
bezier_radius = 0r
# 设置link曲线的颜色
color = blue_a4
# 设置link曲线的厚度
thickness = 2
<rules>
<rule>
condition = var(chr1) eq "ath1"
color=rdylgn-5-div-1
</rule>
<rule>
condition = var(chr1) eq "ath2"
color=rdylgn-5-div-2
</rule>
<rule>
condition = var(chr1) eq "ath3"
color=rdylgn-5-div-3
</rule>
<rule>
condition = var(chr1) eq "ath4"
color=rdylgn-5-div-4
</rule>
<rule>
condition = var(chr1) eq "ath5"
color=rdylgn-5-div-5
</rule>
</rules>
</link>
</links>
总配置文件 circos.conf
karyotype = data/karyotype/mitogenome.txt
chromosomes_units = 1000
chromosomes_display_default = yes
<<include ideogram.conf>>
<<include links.conf>>
<links>
<link>
ribbon = yes
file = data/karyotype/links.txt
radius = 0.999r
bezier_radius = 0r
color = green
stroke_color = green
stroke_thickness = 2
</link>
</links>
<image>
<<include etc/image.conf>>
file* = vars.png
</image>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
- 将data文件导入~/anaconda3/pkgs/circos-0.69.8-0/data//karyotype 文件夹
将配置文件导入~/anaconda3/pkgs/circos-0.69.8-0/etc 文件夹中 - 运行
cd /home/tanwei/anaconda3/pkgs/circos-0.69.8-0/etc
circos -conf circos.conf
-
结果图
image.png
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