circos 可视化手册-line plot 篇

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line plot在circos中的用法比较简单，示例如下：

对于折线图而言，调整外观的属性有以下4个

1. thickness

thickness 控制线条的粗细

2. color

color 控制线条的颜色

3. fill_color

fill_color控制填充色，在折线的下方进行颜色填充

4. max_gap

在直线图中，会看到如下所示的分割线，max_gap的作用就是设置分割线的间距，max_gap = 1u 代表每隔1个单位画一条分割线，其用法和ticks类似

控制位置的属性在前面的文章中我们已经介绍过了，这里在重复一遍。

r0和r1分别设置圆环的内径和外径，max和min设置y轴的最大值和最小值，orientation控制y轴0点的位置，orientation = in代表 y = 0 位于r1上；orientation = out表示y = 0位于r0 上；z代表优先级，数值越大，优先级越高，当两个折线图重叠时，优先级高的会有先显示。

与backgrounds, axes, rules的结合使用，在scatter plot中，我们也介绍过了，今天解锁一种axes的新用法，代码如下

在之前的文章中，我们看到了用y0, y1指定范围，再用spacing参数设定间隔的用法, 这种用法可以方便的设置多条轴线；今天的这个例子中，通过position直接设置轴线的位置，适合指定单条轴线。

最后放一张line plot的示例，在下图中，除去染色体外，包括3个line plot; 最内圈的line plot有3种填充色，背景色也有3种，另外两圈的line plot中，其axes的定义就是使用了position的用法，可以看到其轴线非常少，只有2,3条；最内圈的line plot的轴线则采用spacing的用法，其轴线非常多，而且均匀分布

完整代码如下

<<include colors_fonts_patterns.conf>><<include ideogram.conf>>
<<include ticks.conf>><image>
<<include etc/image.conf>>
</image>karyotype   = data/karyotype/karyotype.human.txtchromosomes_units = 1000000
chromosomes       = hs1 # ;hs2;hs3
chromosomes_display_default = no<plots>type      = line
thickness = 2<plot>max_gap = 1u
file    = data/6/snp.density.250kb.txt
color   = vdgrey
min     = 0
max     = 0.015
r0      = 0.5r
r1      = 0.8rfill_color = vdgrey_a3<backgrounds>
<background>
color     = vvlgreen
y0        = 0.006
</background>
<background>
color     = vvlred
y1        = 0.002
</background>
</backgrounds><axes>
<axis>
color     = lgrey_a2
thickness = 1
spacing   = 0.025r
</axis>
</axes><rules><rule>
condition    = var(value) > 0.006
color        = dgreen
fill_color   = dgreen_a1
</rule><rule>
condition    = var(value) < 0.002
color        = dred
fill_color   = dred_a1
</rule></rules></plot># outside the circle, oriented out
<plot>max_gap = 1u
file    = data/6/snp.density.txt
color   = black
min     = 0
max     = 0.015
r0      = 1.075r
r1      = 1.15r
thickness = 1fill_color = black_a4<axes>
<axis>
color     = lgreen
thickness = 2
position  = 0.006
</axis>
<axis>
color     = lred
thickness = 2
position  = 0.002
</axis>
</axes></plot><plot>
z       = 5
max_gap = 1u
file    = data/6/snp.density.1mb.txt
color   = red
fill_color = red_a4
min     = 0
max     = 0.015
r0      = 1.075r
r1      = 1.15r
</plot># same plot, but inside the circle, oriented in
<plot>
max_gap = 1u
file    = data/6/snp.density.txt
color   = black
fill_color = black_a4
min     = 0
max     = 0.015
r0      = 0.85r
r1      = 0.95r
thickness   = 1
orientation = in<axes><axis>
color     = lgreen
thickness = 2
position  = 0.01
</axis><axis>
color     = vlgreen
thickness = 2
position  = 0.008
</axis></axes><axis>
color     = vlgreen
thickness = 2
position  = 0.006
</axis>
<axis>
color     = red
thickness = 2
position  = 0.002
</axis>
</axes></plot><plot>
z       = 5
max_gap = 1u
file    = data/6/snp.density.1mb.txt
color   = red
fill_color = red_a4
min     = 0
max     = 0.015
r0      = 0.85r
r1      = 0.95r
orientation = in
</plot></plots><<include etc/housekeeping.conf>>

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