1,下载circos,http://circos.ca/software/download/circos/,放置到常用文件夹;
2,选择文件中的circos命令,并添加到Mac的bin文件夹中,使得circos命令可用,类似于pip、conda等命令,如下图:
添加方法:
已知circos文件如下:
终端执行命令:
export PATH=$PATH:`pwd`/circos-0.69-9/bin
3,终端使用,列出circos依赖的Perl包命令:circos -module
上图仅显示部分module结果;
4,若显示missing,则需安装;
先进去:perl -MCPAN -e shell
安装module:install XXX
5,最简单出图
把下面的内容存储到任意目录下的任意文件比如ehbio.conf下,然后运行circos -conf ehbio.conf就可以获得circos的图circos.png和circos.svg。(建议在终端常用工作目录中使用circos命令)
ehbio.conf内容(引用如下):
karyotype = data/karyotype/karyotype.human.txt
<ideogram>
<spacing>
default = 0.005r
</spacing>
radius = 0.9r
thickness = 20p
fill = yes
</ideogram>
################################################################
# The remaining content is standard and required. It is imported
# from default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files,
# look in etc/ in the Circos distribution.
<image>
# Included from Circos distribution.
<<include etc/image.conf>>
</image>
# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
# Included from Circos distribution.
<<include etc/colors_fonts_patterns.conf>>
# Debugging, I/O an dother system parameters
# Included from Circos distribution.
<<include etc/housekeeping.conf>>
6,结果显示如下即可: