想画下图中的下半部分,基因组不同位置的重组率
ref: https://doi.org/10.1038/s41588-023-01548-y (Fig. 2d)
#对文件进行一些文本处理
head -n 1 Per.RUS.beagle.PREDICT.txt | cut -f1,2,3,5 > tmp.head
cat Per.RUS.beagle.PREDICT.txt | grep -v 'recombRate' > tmp
awk '{print $1"\t"$2"\t"$2+1"\t"$5}' tmp > tmp1
awk '{print $1"\t"$3-1"\t"$3"\t"$5}' tmp > tmp2
cat tmp1 tmp2 | sort -Vk 1 > tmp3
cat tmp.head tmp3 > Per.RUS.onlyforplot.rho.txt
开始画图
##In R
library(tidyverse)
RUSrho = read.table("Per.RUS.onlyforplot.rho.txt",header = T, sep = '\t')
RUSrho %>% filter(chrom==17) -> RUSrho #筛选17号染色体
ggplot() +
geom_line(data = RUSrho, mapping = aes(x = start, y = recombRate),color = '#f8766c') +
theme_classic() +
#xlim(0, 5612078) +
labs(x = "position (bp)", y = "recombination rate (c/bp)") +
theme(text=element_text(size=18,face = "plain", color = 'black')) + #坐标轴标题的修改
theme(axis.text=element_text(size=14,color='black')) + #坐标轴刻度文本的修改
theme(axis.line=element_line(color='black',size=0.8)) +
#geom_vline(aes(xintercept= 1195888),linetype=5,col="red")#+
#geom_vline(aes(xintercept= 1245941),linetype=5,col="red")
结果如下图: