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====染色体上 Reads 分布图====

参考链接：

https://www.zhihu.com/question/578473021/answer/2889416571

具体步骤：

<code>
bedtools makewindows -b genome.gtf -w 1000 > genome.window.bed

awk '{print $1"\t"$2"\t"$3"\t0\t0\t+\n"$1"\t"$2"\t"$3"\t0\t0\t-"}'  genome.window.bed >  genome.window.bed.region

#每一个样本运行：

bedtools bamtobed -i hisat2.bam   > hisat2.bed

bedtools coverage -S -a genome.window.bed.region -b hisat2.bed > genome.window.bed.region.cov

</code>

最后画图：

<code>

data <- read.table("/ssd1/wy/workspace/RNA-seq/workspace/resources/genome.window.bed.region.cov",sep="\t")
library(tidyverse)
data <- data  |>
    mutate(log=case_when(V6=="+"~log2(V7+1),
    V6!="+"~ -log2(V7+1)))

chr <-c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY") #因为人类染色体还有很多非常规染色体，如果全部画出来会不好看，所有此处只画出常规染色体。也可以在文件hg19.txt里面只输入常规染色体。data2<- data[data$V1 %in% chr,]
data2<- data[data$V1 %in% c(c(1:20),"X","Y","MT"),]
color <- c("+"="#008B00","-"="#FF8247") # 定义正负链颜色
png(file="a.png")
ggplot(data2)+
    facet_grid(V1~.)+
    geom_point(aes(V2/1000000,log,colour=V6),size=1)+
    theme(
    strip.text.y=element_text(angle=0,face="bold",hjust=0),
    legend.position="none",panel.grid.minor=element_blank(),
    panel.grid.major=element_blank(),
    plot.title=element_text(size=20,face="bold"),
    axis.text.y=element_text(size=10,angle=50,face="bold"),
    strip.background=element_blank(),
    panel.background=element_rect(fill="white"),
    axis.line=element_line(linetype=1))+
    scale_colour_manual(values=color)+
    scale_y_continuous(breaks=c(-15,15))+
    labs(title="Reads Density in Chromosomes")+
    xlab("chromosome position(Mb)")+
    ylab("reads density(log2)")
dev.off()
</code>

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