# MESSAGE -----------------------------------------------------------------

#

# author: Yulin Lyu

# email: lvyulin@pku.edu.cn

#

# require: R whatever

#

# ---

# * 1. Load packages ------------------------------------------------------

setwd("exampleData/ATAC")

# grammar

library(tidyverse)

library(magrittr)

library(glue)

library(data.table)

library(GenomicRanges)

# graphics

library(ggplot2)

library(ggchicklet)

library(ggsci)

library(scales)

# * 2. Load data ----------------------------------------------------------

peakAnnoList <- readRDS("peakAnnoList.rds")

# * 3. Plot ---------------------------------------------------------------

plotData <- imap(peakAnnoList, ~ {as.data.table(.x@anno)[, group := .y][, .(annotation, group)]}) %>% purrr::reduce(rbind)

plotData[str_detect(annotation, "Exon"), annotation := "Exon"]

plotData[str_detect(annotation, "Intron"), annotation := "Intron"]

plotData[str_detect(annotation, "Downstream|Intergenic"), annotation := "Intergenic"]

plotData <- plotData[, .N, by = .(annotation, group)]

ggplot(plotData, aes(x = group, y = N)) +

  geom_chicklet(aes(fill = fct_rev(annotation)), position = "fill", width = .95) +

  scale_fill_nejm() +

  scale_y_continuous(expand = c(0, 0)) +

  coord_flip() +

  labs(x = "", y = "") +

  theme(

    aspect.ratio = .5,

    panel.background = element_blank(),

    panel.grid = element_blank(),

    axis.line = element_line(),

    legend.title = element_blank()

  )

ggsave("graphics/peakAnnoDisp.png", width = 5, height = 2.5)