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002.Figure 1D (Distance for ACRs to TSS).md

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Distance for ACRs to TSS

library(ggplot2)
library(ggpointdensity) 
library(viridis)
library("ChIPseeker")
library("GenomicFeatures")



poppy_TxDb <- makeTxDbFromGFF("D:/001poppy_atac_new_genome/Papaver_somniferum.gene.gff3")
setwd("D:/001poppy_atac_new_genome/ATAC_peak/")
files <- list.files(pattern = "*.narrowPeak")
files_list <- as.list(files)
names(files_list) <- c("Capsule","Petal","Stem","Fine_Root","Leaf","Tap_Root")
peakAnnoList <- lapply(files_list, annotatePeak, TxDb=poppy_TxDb,
                       tssRegion=c(-3000, 3000), verbose=FALSE)

plotDistToTSS(peakAnnoList,ylab = "Opening sites (%) (5'->3')",
              title = paste0("Distribution of opening loci relative to TSS"))