# 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)

# graphics

library(ggplot2)

library(ggrepel)

library(scales)

library(latex2exp)

library(patchwork)

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

motifFile <- list.files("motif", "known", full.names = T)

motifGroup <- str_remove_all(motifFile, ".*/|_.*")

motifData <- map(motifFile, fread) %>% set_names(motifGroup)

motifMeta <- fread("../../data/motifTable.txt", sep = "\t")

motifMeta[Symbol == "", Symbol := `Factor Name`][]

name2symbol <- structure(

  motifMeta$Symbol,

  names = motifMeta$Name

)

motifData <- map(motifData, ~ {.x[, symbol := name2symbol[`Motif Name`]]})

motifData <- map(motifData, ~ {.x[is.na(symbol), symbol := str_remove(`Motif Name`, "/.*") %>% str_remove("\\(.*")]})

motifData <- map(motifData, ~ {.x[, symbol := toupper(symbol)]})

motifData <- map(motifData, ~ {.x[, p := -log10(`P-value`)]})

saveRDS(motifData$g1[, .(`Motif Name`, symbol)], "motifAnno.rds")

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

plotList <- imap(motifData, ~ (

  ggplot(.x, aes(x = seq_along(p), y = p)) +

    geom_point(aes(size = p), show.legend = F) +

    geom_text_repel(

      data = .x[1:15], aes(label = symbol),

      nudge_x = 10, size = 3, fontface = 3, segment.size = .3, segment.alpha = .5) +

    scale_radius(range = c(.1, 2)) +

    labs(x = "order", y = TeX("$-log_{10}(\\textit{P}\\,value)$"), title = .y) +

    theme(

      aspect.ratio = 1,

      panel.background = element_blank(),

      panel.grid = element_blank(),

      axis.line = element_line()

    )

))

reduce(plotList, `+`) + plot_layout(ncol = 1)

ggsave("graphics/motifEnrich.png", width = 4, height = length(motifData) * 4)