# 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(ComplexHeatmap)

library(circlize)

library(RColorBrewer)

library(ggsci)

library(scales)

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

peakData <- fread("peak/peak_value.txt", skip = 3)

peakGroup <- readRDS("peakGroup.rds")

sample <- rep(c("F", "P", "XF"), each = 300) %>% factor(levels = c("P", "F", "XF"))

peakType <- rep(c("g1", "g4"), c(length(peakGroup$`1`), length(peakGroup$`4`))) %>% factor(levels = c("g4", "g1"))

heatData <- as.matrix(peakData)

heatData[is.nan(heatData)] <- 0

max(heatData)

colorFun <- colorRamp2(seq(6, 0, len = 11), brewer.pal(11, "Spectral"))

p <- Heatmap(

  heatData, border = F, col = colorFun,

  cluster_rows = F, cluster_columns = F,

  show_row_names = F, show_column_names = F,

  column_title_side = "bottom",

  row_split = peakType,

  column_split = sample,

  left_annotation = rowAnnotation(

    type = anno_block(

      gp = gpar(col = NA, fill = pal_nejm()(2)[2:1]),

      width = unit(.1, "in"))

  ),

  heatmap_legend_param = list(

    title = "Normalized signal",

    title_position = "lefttop-rot",

    legend_height = unit(2, "in")),

  width = unit(4, "in"),

  height = unit(8, "in")

)

png("graphics/heatmapTrack.png", res = 300, width = 6, height = 9, units = "in")

p

dev.off()