【三维基因组】PyGenomeTrack之AB compartment可视化

image.png

前期的时候，我们画ABcompartment 往往需要个性化嵌入以下代码：

ax.fill_between(mat['start'], 0, mat[eigen],where=mat[eigen]>= 0, facecolor=color1)
ax.fill_between(mat['start'], 0, mat[eigen],where=mat[eigen] < 0, facecolor=color2)

自从研究了pyGenomeTrack之后，发现pyGenomeTrack也能实现ABcompartment的画法，哈哈哈，真是方便呐～～
具体实现方法如下：

pyGenomeTracks  --tracks  config.ini --region chr10:0-150982314 --outFileName   chr10_40000_AB_minus.pdf  --width 22 --height 20

其核心需要配置config.ini ,那么我们来看一眼config的内容：

[x-axis]
where = top
#color = #0000FF
#color = #DE8BF9
#color = #0F99B2

[test bedgraph]
file = sam1_Acom.bg
height = 1
color=#F0EA3A
title = sam1
min_value=0
max_value=1.5

[test bedgraph]
file=sam1_Bcom.bg
height=1
color=#204BA0
min_value=-1.5
max_value=0
            
[test bedgraph]
file = sam2_Acom.bg
height = 1
color=#F0EA3A
title = sam2
min_value=0
max_value=1.5

[test bedgraph]
file=sam2_Bcom.bg
height=1
color=#204BA0
min_value=-1.5
max_value=0
            
[test bedgraph]
file = sam3_Acom.bg
height = 1
color=#F0EA3A
title = sam3
min_value=0
max_value=1.5

[test bedgraph]
file=sam3_Bcom.bg
height=1
color=#204BA0
min_value=-1.5
max_value=0
            
[test bedgraph]
file = sam2-sam1_Acom.bg
height = 1
color=#F0EA3A
title = sam2-sam1
min_value=0
max_value=2.5

[test bedgraph]
file=sam2-sam1_Bcom.bg
height=1
color=#204BA0
min_value=-2.5
max_value=0
            
[test bedgraph]
file = sam3-sam1_Acom.bg
height = 1
color=#F0EA3A
title = sam3-sam1
min_value=0
max_value=2.5

[test bedgraph]
file=sam3-sam1_Bcom.bg
height=1
color=#204BA0
min_value=-2.5
max_value=0
            
[test bedgraph]
file = sam2-sam1_Acom.bg
height = 1
color=#F0EA3A
title = sam3-sam2
min_value=0
max_value=2.5

[test bedgraph]
file=sam2-sam1_Bcom.bg
height=1
color=#204BA0
min_value=-2.5
max_value=0

config中核心文件 Acom.bg(pc1>0)格式如下:
总共4列 chr start end pc1

chr10   40000   80000   0.028098
chr10   80000   120000  0.115531
chr10   800000  840000  0.391115
chr10   3080000 3120000 0.288466
chr10   3200000 3240000 0.0274775
chr10   3320000 3360000 0.118719
chr10   6440000 6480000 0.0658824
chr10   6560000 6600000 0.05398390000000001
chr10   7000000 7040000 0.35875300000000004
chr10   7160000 7200000 0.233938

config中核心文件 B com.bg(pc1<0)格式如下:
总共4列 chr start end pc1

chr10   120000  160000  -0.060273000000000077
chr10   240000  280000  -0.006977999999999984
chr10   360000  400000  -0.32917830000000003
chr10   520000  560000  -0.082446
chr10   600000  640000  -0.120475
chr10   760000  800000  -0.08050699999999994
chr10   880000  920000  -0.06900700000000004
chr10   1240000 1280000 -0.08115699999999992
chr10   1360000 1400000 -0.181178
chr10   1400000 1440000 -0.008543000000000078

配置完成之后就大功告成了，来简单看一下效果～～

image.png

最后编辑于：2020.07.13 10:45:19