# Load required packages
suppressPackageStartupMessages(library(grid))
suppressPackageStartupMessages(library(ComplexHeatmap))
suppressPackageStartupMessages(library(circlize))
suppressPackageStartupMessages(library(RColorBrewer))
suppressPackageStartupMessages(library(dendextend))
suppressPackageStartupMessages(library(dendsort))
suppressPackageStartupMessages(library(gridBase))

# Get arguments from the command line
args=commandArgs(T);

# Check the number of arguments
if (length(args) != 2) {
  stop("Please provide two arguments: the input CSV file path and the output PDF file path.", call. = FALSE)
}

# Get the input CSV file path and the output PDF file path
input_csv <- args[1]
output_pdf <- args[2]

# Check if the input file exists
if (!file.exists(input_csv)) {
  stop("The input file does not exist. Please check the file path.", call. = FALSE)
}

# Load the data for plotting
data <- read.table(file = input_csv, header = TRUE, row.names = 1, sep = ',')

# View the data
message("Data loaded successfully. The first few rows are as follows:")
print(head(data))

# Convert to matrix format and normalize the data
data <- as.matrix(data)
cir1 <- t(scale(t(data)))

# Handle NA values
cir1[is.na(cir1)] <- 0

# View the normalized data
message("Data normalization successful. The first few rows are as follows:")
print(head(cir1))

# Define the color gradient for the heatmap
mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))

# Open the PDF device
pdf(output_pdf, width = 10, height = 8)

# Draw the basic circular heatmap
message("Drawing the basic circular heatmap...")
circos.heatmap(cir1, col = mycol)
circos.clear()

# Adjust and beautify the circular heatmap in circos.heatmap()
message("Drawing the adjusted and beautified circular heatmap...")
circos.par(gap.after = c(30))
circos.heatmap(cir1, col = mycol,
               dend.side = "inside",
               rownames.side = "outside",
               rownames.col = "black",
               rownames.cex = 1.2,
               rownames.font = 1.2,
               bg.border = "black",
               cluster = TRUE)
circos.clear()

# Adjust and beautify the dendrogram
message("Drawing the circular heatmap with adjusted and beautified dendrogram...")
circos.par(gap.after = c(30))
circos.heatmap(cir1, col = mycol, dend.side = "inside",
               rownames.side = "outside",
               track.height = 0.28,
               rownames.col = "black",
               rownames.cex = 1.3,
               rownames.font = 1.3,
               cluster = TRUE,
               dend.track.height = 0.18,
               dend.callback = function(dend, m, si) {
                 color_branches(dend, k = 15, col = 1:15)
               })
circos.clear()

# Add legend labels
message("Adding legend labels...")
lg <- Legend(title = "Exp", col_fun = mycol,
             direction = c("vertical"))
grid.draw(lg)

# Add column names
message("Adding column names...")
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
  if (CELL_META$sector.numeric.index == 1) {
    cn <- colnames(cir1)
    n <- length(cn)
    circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"),
                1:n + 5,
                cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
  }
}, bg.border = NA)

circos.clear()

# Close the PDF device
dev.off()

message("The heatmap has been successfully saved to: ", output_pdf)