add 优化R脚本

res/heatmap_script.R

@@ -1,27 +1,27 @@
-# Load required packages
+# 加载所需的包
 suppressPackageStartupMessages(library(circlize))
 suppressPackageStartupMessages(library(RColorBrewer))
 suppressPackageStartupMessages(library(ComplexHeatmap))
 suppressPackageStartupMessages(library(dendextend))
 
-# Get arguments from the command line
+# 获取命令行参数
 args <- commandArgs(trailingOnly = TRUE)
 
-# Check the number of arguments
+# 检查参数数量
 if (length(args) != 2) {
-  stop("Please provide two arguments: the input CSV file path and the output PDF file path.", call. = FALSE)
+  stop("请提供两个参数：输入CSV文件路径和输出PDF文件路径。", call. = FALSE)
 }
 
-# Get the input CSV file path and the output PDF file path
+# 获取输入CSV文件路径和输出PDF文件路径
 input_csv <- args[1]
 output_pdf <- args[2]
 
-# Check if the input file exists
+# 检查输入文件是否存在
 if (!file.exists(input_csv)) {
-  stop("The input file does not exist. Please check the file path.", call. = FALSE)
+  stop("输入文件不存在。请检查文件路径。", call. = FALSE)
 }
 
-# Function to load and preprocess data
+# 函数加载和预处理数据
 load_and_preprocess_data <- function(file_path) {
   data <- read.table(file = file_path, header = TRUE, row.names = 1, sep = ',')
   data_matrix <- as.matrix(data)
@@ -30,31 +30,37 @@ load_and_preprocess_data <- function(file_path) {
   return(normalized_data)
 }
 
-# Load and preprocess data
+# 加载和预处理数据
 cir1 <- load_and_preprocess_data(input_csv)
 
-# Define the color gradient for the heatmap
+# 打印数据维度和头部
+print(dim(cir1))
+print(head(cir1))
+
+# 定义颜色梯度
 mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
 
-# Open the PDF device
-pdf(output_pdf, width = 10, height = 8)
+# 打开PDF设备，设置宽度和高度相等
+pdf(output_pdf, width = 8, height = 8)
 
-# Draw the adjusted and beautified circular heatmap
+# 设置绘图参数
 circos.par(gap.after = c(30))
+
+# 绘制调整后的圆形热图
 circos.heatmap(cir1, 
                 col = mycol, 
                 dend.side = "inside", 
                 rownames.side = "outside", 
                 rownames.col = "black", 
                 rownames.cex = 1.3, 
-                track.height = 0.35, 
+                track.height = 0.35,  # 增加轨道高度
                 cluster = TRUE, 
                 dend.track.height = 0.18, 
                 dend.callback = function(dend, m, si) {
                   color_branches(dend, k = 15, col = 1:15)
                 })
 
-# Add column names
+# 添加列名
 circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
   if (CELL_META$sector.numeric.index == 1) {
     cn <- colnames(cir1)
@@ -65,14 +71,14 @@ circos.track(track.index = get.current.track.index(), panel.fun = function(x, y)
   }
 }, bg.border = NA)
 
-# Add legend
+# 添加图例
 lg <- Legend(title = "Exp", col_fun = mycol, direction = "vertical")
 grid.draw(lg)
 
-# Clear the circular plot
+# 清除圆形图
 circos.clear()
 
-# Close the PDF device
+# 关闭PDF设备
 dev.off()
 
-message("The heatmap has been successfully saved to: ", output_pdf)
+message("热图已成功保存至: ", output_pdf)