阿狗工具

1.计算Tajima's D

通过vcftools对不同物种的Tajima'D进行滑窗计算:

vcftools --vcf str.vcf --out pop1.tajimaD --TajimaD 500000 --keep pop1.txt

vcftools --vcf str.vcf --out pop2.tajimaD --TajimaD 500000 --keep pop2.txt

#绘制Tajima D windows=500000kb

library(ggplot2)

2.在R中读取TajimaD文件

pop1_tajimaD<-read.table("vcftools/pop1.tajimaD.Tajima.D",header = T)

pop2_tajimaD<-read.table("vcftools/pop2.tajimaD.Tajima.D",header = T)

3.删除空值并将两个结果进行合并

pop1_tajimaD1<-na.omit(pop1_tajimaD)

pop2_tajimaD1<-na.omit(pop2_tajimaD)

pop1_tajimaD1$species <- "Species1"

pop2_tajimaD1$species <- "Species2"

merge <- rbind(pop1_tajimaD1,pop2_tajimaD1)

4.绘图

ggplot(sll,aes(x=species,y=TajimaD,color=species,fill=species))+

  scale_y_continuous(breaks=-2:4)+

  scale_color_manual(values = my_pal,guide="none")+

  scale_fill_manual(values = my_pal,guide="none")+

  stat_boxplot(geom = "errorbar",width=0.2,size=1)+

  geom_boxplot(width=0.2,fill="white",size=1,outlier.shape = NA)+  #绘制箱线图

  gghalves::geom_half_violin(aes(fill=species),alpha=0.5,size=1,side = "r",position = position_nudge(x = .15, y = 0))+  #绘制小提琴图

  gghalves::geom_half_point(aes(fill=species),side = "l",range_scale = 0.3,alpha=0.5,size=1)+  #绘制点图

  labs(x="Species",y="TajimaD")+ theme_bw()+  

  theme(legend.title = element_blank(),  

        legend.background = element_blank(),  

        #legend.key = element_blank(), 

        panel.grid.major = element_blank(),  

        panel.grid.minor = element_blank(),  

        legend.position='right')