大家好，很高兴又跟大家见面了，上一周我们画出了一个看起来还不错的基因组圈图，但是跟我们的目标还是有一些差距，所以今天我将把该图的终极画法写出来，供大家参考。

紧接着上一周的图形，我们缺少两个信息，一个是GC含量的图示，还有一个是GC偏移的信息。GC含量可能大家都能理解，GC偏移又是什么呢？首先给出公式：GC偏移=（G-C）/（G+C）这个式子用来衡量G和C的相对含量，如果G>C则GC skew的值为正值，G<C则为负值。在大多数细菌基因组中，前导链(leading strand)和滞后链(lagging strand)在碱基组成上有明显的不同——前导链富含G和T，但是滞后链中的A和C则更多一些。打破A=T和C=G的碱基频率发生的偏移，被称之为“AT(AT-skew)”和“GC(GC-skew)”。由于通常GC偏移比AT偏移发生的更明显，所以习惯上更多地只考虑GC偏移。

我们在每条scaffold 上以1000bp 为一个窗口，计算GC 含量减去全基因组Average_GC>=0 的输出到positive_gc_count.txt， <0 的输出到negative_gc_count.txt ； GC 偏移： (G-C)/(G+C) >=0 的输出到positive_gc_skew.txt， <0 的输出到negative_gc_skew.txt。比如这样：

scaffold1 1 1000 0.0940111701086518

scaffold1 1001 2000 0.0980111701086517

scaffold1 2001 3000 0.0790111701086518

scaffold1 3001 4000 0.0450111701086518

scaffold1 4001 5000 0.102011170108652

我们再一次打开circos.conf配置文件我们在后面加入这几行：

<plots>

type = line

thickness = 1p

<plot>

z = 2

max_gap = 0u

file = positive_gc_count.txt

color = red

fill_color = red

r0 = 0.48r

r1 = 0.57r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = negative_gc_count.txt

color = blue

fill_color = blue

r0 = 0.39r

r1 = 0.48r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = positive_gc_skew.txt

color = aquamarine

fill_color = aquamarine

r0 = 0.27r

r1 = 0.36r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = negative_gc_skew.txt

color = orange

fill_color = orange

r0 = 0.18r

r1 = 0.27r

orientation = out

</plot>

</plots>

就这样，我们把这个圈图就画得很帅啦!如图所示：

很有成就感是不是。

有些小伙伴问我图例和文字是怎么加进去的，这可能需要你掌握一些SVG的作图技巧了，如果有机会的话，我会在将来对这一块有详细的解释。按照惯例，我把这个图形的所有代码都列在下面，如果需要对图形进行调整，可以自行修改代码：

<<includeetc/colors_fonts_patterns.conf>>

<image>

<<includeetc/image.conf>>

</image>

karyotype = karyotype.txt

chromosomes_units = 100000

chromosomes_display_default = yes

<ideogram>

<spacing>

default = 0.005r

</spacing>

radius = 0.80r

thickness = 6p

fill = yes

fill_color = deepskyblue

stroke_color = black

stroke_thickness = 1p

show_label = yes

label_font = light

label_radius = 1r + 110p

label_size = 30

label_parallel = no

</ideogram>

show_ticks = yes

show_tick_labels = yes

<ticks>

skip_first_label = no

skip_last_label = no

radius = dims(ideogram,radius_outer)

color = black

thickness = 2p

size = 30p

multiplier = 1e-6

format = %.2f

<tick>

spacing = 20000b

size = 10p

show_label = no

thickness = 3p

</tick>

<tick>

spacing = 100000b

size = 20p

show_label = yes

label_size = 25p

label_offset = 10p

format = %.2f

</tick>

</ticks>

<highlights>

z = 0

<highlight>

file = sensegene.gff

r0 = 0.90r

r1 = 0.99r

fill_color = 169,169,169

</highlight>

<highlight>

file = temp.txt

r0 = 0.90r

r1 = 0.901r

fill_color = black

</highlight>

<highlight>

file = antigene.gff

r0 = 0.81r

r1 = 0.90r

fill_color = 169,169,169

</highlight>

<highlight>

file = sense_strand_ncRNA.txt

r0 = 0.69r

r1 = 0.78r

</highlight>

<highlight>

file = temp.txt

r0 = 0.69r

r1 = 0.691r

fill_color = black

</highlight>

<highlight>

file = antisense_strand_ncRNA.txt

r0 = 0.60r

r1 = 0.69r

</highlight>

</highlights>

<plots>

type = line

thickness = 1p

<plot>

z = 2

max_gap = 0u

file = positive_gc_count.txt

color = red

fill_color = red

r0 = 0.48r

r1 = 0.57r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = negative_gc_count.txt

color = blue

fill_color = blue

r0 = 0.39r

r1 = 0.48r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = positive_gc_skew.txt

color = aquamarine

fill_color = aquamarine

r0 = 0.27r

r1 = 0.36r

orientation = out

</plot>

<plot>

z = 2

max_gap = 0u

file = negative_gc_skew.txt

color = orange

fill_color = orange

r0 = 0.18r

r1 = 0.27r

orientation = out

</plot>

</plots>

<<includeetc/housekeeping.conf>>

新年快要到了，在这里，祝愿所有的小伙伴新年快乐，学习进步。如果大家有什么想要跟我交流的，可以在后台发送问题，我会尽我所能为大家讲解。

下一周我就回家啦，我今年的更新就到这里了。我们明年在见！