By masiyi, 5 August, 2024
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一、准备工作

使用MCScanX得到 .collinearity共线性结果文件，并且按照其要求处理得到特定的 .gff注释文件，这里均以os_sb测试

二、可视化结果

首先准备绘图配置文件 .ctl，文件内容如下（其中参数根据具体需求自行修改）：

1500    //dimension (in pixels) of the x-axis
1500    //dimension (in pixels) of the y-axis
os1,os2,os3,os4,os5,os6,os7,os8,os9,os10,os11,os12      //chromosomes in x-axis
sb1,sb2,sb3,sb4,sb5,sb6,sb7,sb8,sb9,sb10        //chromosomes in y-axis

1.dual synteny plots

[root@6e43d822f3bf os_sb]# java ../../downstream_analyses/dual_synteny_plotter.java -g os_sb.gff -s os_sb.collinearity -c os_sb.ctl -o os_sb_synteny.png

PS：这里需要注意上面的 .ctl文件分隔符必须是tab符号，否则这里的操作会报错：

[root@6e43d822f3bf os_sb]# java ../../downstream_analyses/dual_synteny_plotter.java -g os_sb.gff -s os_sb.collinearity -c os_sb.ctl -o os_sb_synteny.png
Reading control file error: For input string: "550 //dimension (in pixels) of the x-axis "
Exception in thread "main" java.lang.IllegalArgumentException: Width (0) and height (0) cannot be <= 0
	at java.desktop/java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:1016)
	at java.desktop/java.awt.image.BufferedImage.<init>(BufferedImage.java:333)
	at dual_synteny_plotter.main(dual_synteny_plotter.java:263)

2.dot plots

[root@6e43d822f3bf os_sb]# java ../../downstream_analyses/dot_plotter.java -g os_sb.gff -s os_sb.collinearity -c os_sb.ctl -o os_sb_dot.png

 

3.circle plots

这里需要写一个新的 .ctl文件：

2000    //plot width and height (in pixels)
sb1,sb2,sb3,sb4,sb5,sb6,sb7,sb8,sb9,sb10,os1,os2,os3,os4,os5,os6,os7,os8,os9,os10,os11,os12     //chromosomes in the circle

分隔符要求同上，依然要求tab分隔符，绘图：

[root@6e43d822f3bf os_sb]# java ../../downstream_analyses/circle_plotter.java -g os_sb.gff -s os_sb.collinearity -c os_sb.ctl -o os_sb_circle.png