circos 可视化手册-scatter plot 篇
circos 可视化手册-scatter plot 篇
plots这个block 中，支持许多的图表类型，scatter plot是最常用的一种。用法如下：
关于file文件的内容，在之前的文章中已经详细介绍过。r0和r1定义圆环的位置，max和min定义y轴的最小值和最大值，剩余的几个参数控制散点的外观。
glyph表示点的形状，circle代表圆形，triangle代表三角形，rectangle代表矩形；glyph_size控制点的大小；fill_color控制点的填充色，stroke_color控制边框的颜色。
关于scatter plot, 在软件的安装目录下，有对应的默认配置
etc/tracks/scatter.conf
oritenation表示方向，in表示从r0到r1, out表示从r1到r0
在plot中，可以插入backgrounds, axes, rules3种block
1. backgrounds
用法如下:
backgrounds 定义背景色，每个定义一个区域的背景色，这个区域由y0和y1定义。
在plot中， max和min分别定义了y轴的最大值和最小值，这里的y0和y1对应的就是y轴的值；y0代表起始位置，y1代表终止位置；如果只指定了y0和y1中的一个，需要参考邻近区域和max,min的值作出判断
在上图的第一个background中，只指定了y0 = 0.006,从其他结果background的设置可以推测出，此时的y1 = max;
上面的例子中，根据y轴的值划分了3个区域，定义了3种不同 的背景色
- min到0.002，背景色为
vvlred - 0.002到0.006，背景色为
vlgrey - 0.006到max, 背景色为
vvlgreen
2. axes
用法如下：
axes定义y轴的刻度线，由多个axis构成。和backgrounds 一样，根据y0和y1定义区域，spacing定义刻度线的间隔。
刻度线的外观由thickness和color两个参数控制，thickness 控制线条的粗细程度，color控制线条的颜色。
3. rules
用法如下：
rules代表规则，由多个rule构成；在每个rule中，conditioon设置规则，var(value) > 0.006 表示 y轴的值大于0.006，当满足这个条件时，执行rule中的其他语句，下面的示例中，调整了value > 0.006的点的外观。
最后看一个实例
这张图中，除了染色体的圆环外，还有3圈圆环，每一个圆环都是一张scatter plot, 而且都设置了背景色和刻度线。
结合整幅图的结构和散点图的用法，理解下面的配置文件就非常简单了
<<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################################################################
#
# define 3 scatter plots, using the same data file
#<plots># all are scatter plotstype = scatter
stroke_thickness = 1# first plot shows all points and selectively formats points at small/large
# y-axis values to be red/green and triangles/rectangles<plot>file = data/6/snp.density.txt
fill_color = grey
stroke_color = black
glyph = circle
glyph_size = 10max = 0.013
min = 0
r1 = 0.95r
r0 = 0.65r# optional y0/y1 values (absolute or relative) in <background> blocks
# define the start/end limits of background color
#
# y0 = 0.006
# y0 = 0.75r<backgrounds>
<background>
color = vvlgreen
y0 = 0.006
</background>
<background>
color = vlgrey
y1 = 0.006
y0 = 0.002
</background>
<background>
color = vvlred
y1 = 0.002
</background>
</backgrounds><axes>
<axis>
color = lgreen
thickness = 1
spacing = 0.05r
y0 = 0.006
</axis>
<axis>
color = dgreen
thickness = 2
spacing = 0.1r
y0 = 0.006
</axis><axis>
color = lgrey
thickness = 1
spacing = 0.05r
y1 = 0.006
y0 = 0.002
</axis>
<axis>
color = dgrey
thickness = 2
spacing = 0.1r
y1 = 0.006
y0 = 0.002
</axis><axis>
color = lred
thickness = 1
spacing = 0.05r
y1 = 0.002
</axis><axis>
color = dred
thickness = 2
spacing = 0.1r
y1 = 0.002
</axis></axes><rules><rule>
condition = var(value) > 0.006
stroke_color = dgreen
fill_color = green
glyph = rectangle
glyph_size = 8
</rule><rule>
condition = var(value) < 0.002
stroke_color = dred
fill_color = red
glyph = triangle
</rule></rules></plot># the second plot is a crop of the first plot, placed outside
# the ideogram circle, showing only points with large y-values<plot>file = data/6/snp.density.txt
fill_color = green
stroke_color = dgreen
glyph = rectangle
glyph_size = 8max = 0.013
min = 0.007
r1 = 1.175r
r0 = 1.075r<backgrounds>
# you can stack backgrounds by using transparent color
<background>
color = vlgreen_a4
y0 = 0.75r
</background>
<background>
color = vlgreen_a4
y0 = 0.5r
</background>
<background>
color = vlgreen_a4
y0 = 0.25r
</background>
<background>
color = vlgreen_a4
</background>
</backgrounds><axes>
<axis>
color = green_a3
thickness = 2
spacing = 0.1r
</axis>
</axes><rules><rule>
condition = var(value) < 0.007
show = no
</rule></rules></plot># the third plot is a crop of the first plot, placed closer to the
# center of the circle, showing only points with small y-values<plot>file = data/6/snp.density.txt
fill_color = red
stroke_color = dred
glyph = rectangle
glyph_size = 8max = 0.0015
min = 0.000
r1 = 0.60r
r0 = 0.35r<backgrounds>
<background>
color = vlred_a4
y1 = 0.25r
</background>
<background>
color = vlred_a4
y1 = 0.5r
</background>
<background>
color = vlred_a4
y1 = 0.75r
</background>
<background>
color = vlred_a4
</background>
</backgrounds><axes>
<axis>
color = red_a5
thickness = 1
spacing = 0.025r
</axis>
<axis>
color = red_a3
thickness = 2
spacing = 0.1r
</axis>
</axes><rules>
<rule>
condition = var(value) > 0.002
show = no
</rule>
</rules></plot></plots><<include etc/housekeeping.conf>>