上一步最后的circos.conf如下：

karyotype=karyotype.txt
chromosomes_units = 100000
chromosomes_display_default = yes
<ideogram>
<spacing>
default = 0.005r
</spacing>
radius           = 0.80r
thickness        = 6p
fill             = yes
stroke_color     = dgrey
stroke_thickness = 2p
show_label = yes
label_font = default
label_radius = dims(ideogram,radius) + 0.05r
label_size = 46
label_parallel = yes
label_fromat = eval(sprintf("%s",var(chr)))
</ideogram>

show_ticks_labels = yes
show_ticks = yes
<ticks>
color = black
multiplier = 1e-6
radius = 1r
thickness = 2p

<tick>
size = 10p
spacing = 5u
</tick>

<tick>
color = black
format = %d
label_offset = 10p
label_size = 25p
show_label = yes
size = 15p
spacing = 10u
thickness = 4p
</tick>
</ticks>


<image>
dir* = .
radius* = 500p
<<include etc/image.conf>>
</image>

<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>

一：下载拟南芥数据

记得用ensembl的gff，下面是两者的区别。

iensembl的gff
ncbi的gff

# download
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.gff.gz

提取基因的位置信息

zgrep '[[:blank:]]gene[[:blank:]]' GCF_000001735.4_TAIR10.1_genomic.gff.gz | cut -f 1,4,5 | awk '{print "chr"$1"\t"$2"\t"$3}' > genes.bed

接着用bedtools以500kb为滑窗，沿染色体创建窗口

cut -d ' ' -f 3,6 karyotype..txt | tr ' ' '\t' > tair10.genome
bedtools makewindows -g tair10.genome -w 500000 > tair10.windows

最后统计信息

bedtools coverage -a tair10.windows -b genes.bed | cut -f 1-4 > genes_num.txt

最后的genes_num.txt为下一步用于作图的数据。

汇总

二：开始作图

还是用上一步的circos.conf，再加上一部分plot

...
<plots>

<plot>
type      = line
thickness = 2
max_gap = 1u
file = genes_num.txt
color   = redv
r0      = 0.51r
r1      = 0.60r
</plot>

<plot>
type    = heatmap
file    = genes_num.txt
color   = spectral-5-div
r1      = 0.70r
r0      = 0.61r
</plot>

<plot>
type = scatter
fill_color       = grey
stroke_color     = black
glyph            = circle
glyph_size       = 10
file = genes_num.txt
r1   = 0.80r
r0   = 0.71r
</plot>

<plot>
type = histogram
file = genes_num.txt
r1   = 0.89r
r0   = 0.81r
</plot>

</plots>

结果：

拟南芥