CIRCOS教程翻译 1.7——heatmap

heatmap其实博主对这章有一些细节还没有完全理解，照着画倒是可以完成，但是就是心里挺不安的。。。

karyotype = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000

chromosomes_display_default = no
chromosomes                 = /hs[1234]$/

<colors>
chr1* = red
chr2* = orange
chr3* = green
chr4* = blue
</colors>

chromosomes_reverse = /hs[234]/
chromosomes_scale   = hs1=0.5r,/hs[234]/=0.5rn

<plots>
#heatmap的数据格式：hs1 0 1999999 20.0000 id=hs2(或hs1)
#heatmap会将数据中的max和min值当作颜色数组的极限值，每个数据的颜色为c(n)，f = (value - min) / ( max - min )，n = N * f
<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.89r
r0    = 0.88r

#将颜色定义为hs1的颜色过渡集合
color = hs1_a5,hs1_a4,hs1_a3,hs1_a2,hs1_a1,hs1

#如果使用scale_log_base，那么heatmap的颜色过渡不再是线性的，而是指数的，n = N * f**(1/scale_log_base)
#如果scale_log_base > 1，那么接近最小值的颜色动态变化较大；反之scale_log_base < 1，那么接近最大值的颜色动态变化较大
scale_log_base = 5

<rules>
<<include exclude.hs1.rule>>

<rule>
condition = var(id) ne "hs1" #将id不等于hs1的不显示
show      = no
</rule>
</rules>

</plot>

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.90r
r0    = 0.89r
color = hs2_a5,hs2_a4,hs2_a3,hs2_a2,hs2_a1,hs2
scale_log_base = 5

<rules>
<<include exclude.hs1.rule>>
<rule>
condition = var(id) ne "hs2"
show      = no
</rule>
</rules>

</plot>

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.91r
r0    = 0.90r
color = hs3_a5,hs3_a4,hs3_a3,hs3_a2,hs3_a1,hs3
scale_log_base = 5

<rules>
<<include exclude.hs1.rule>>
<rule>
condition = var(id) ne "hs3"
show      = no
</rule>
</rules>

</plot>

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.92r
r0    = 0.91r
color = hs4_a5,hs4_a4,hs4_a3,hs4_a2,hs4_a1,hs4
scale_log_base = 5

<rules>
<<include exclude.hs1.rule>>
<rule>
condition = var(id) ne "hs4"
show      = no
</rule>
</rules>

</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.hist.txt
r1   = 0.88r
r0   = 0.81r

fill_color = vdgrey
extend_bin = no

<rules>
<<include exclude.hs1.rule>>
</rules>

<<include backgrounds.conf>>

</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.stacked.txt
r1   = 0.99r
r0   = 0.92r
fill_color  = hs1,hs2,hs3,hs4
orientation = in
extend_bin  = no

<rules>
<<include exclude.hs1.rule>>
</rules>

<<include axes.conf>>

</plot>

</plots>

<links>

<link>
file          = data/5/segdup.txt
radius        = 0.8r
bezier_radius = 0r
color         = black_a4
thickness     = 2

<rules>
<rule>
condition     = var(intrachr)
show          = no
</rule>
<rule>
condition     = 1
color         = eval(var(chr2))
flow          = continue
</rule>
<rule>
condition     = from(hs1)
radius1       = 0.99r
</rule>
<rule>
condition     = to(hs1)
radius2       = 0.99r
</rule>

</rules>

</link>

</links>

<<include ideogram.conf>>

<<include ticks.conf>>

<image>
<<include etc/image.conf>>                
</image>

<<include etc/colors_fonts_patterns.conf>> 

<<include etc/housekeeping.conf>>