CircosHeatmap-aardio/res/heatmap_script.R

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

# Get arguments from the command line
args <- commandArgs(trailingOnly = TRUE)

# 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)
}

# Function to load and preprocess data
load_and_preprocess_data <- function(file_path) {
  data <- read.table(file = file_path, header = TRUE, row.names = 1, sep = ',')
  data_matrix <- as.matrix(data)
  normalized_data <- t(scale(t(data_matrix)))
  normalized_data[is.na(normalized_data)] <- 0
  return(normalized_data)
}

# Load and preprocess data
cir1 <- load_and_preprocess_data(input_csv)

# 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 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 = 1.3, 
                track.height = 0.35, 
                cluster = TRUE, 
                dend.track.height = 0.18, 
                dend.callback = function(dend, m, si) {
                  color_branches(dend, k = 15, col = 1:15)
                })

# Add 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 + 2.5, 
                cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
  }
}, bg.border = NA)

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

# Clear the circular plot
circos.clear()

# Close the PDF device
dev.off()

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