add 更新代码结构，允许传入输入输出参数

heatmap_script.R

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+# 加载所需的包
+library(grid)
+library(ComplexHeatmap)
+library(circlize)
+library(RColorBrewer)
+library(dendextend)
+library(dendsort)
+library(gridBase)
+
+# 从命令行获取参数
+args <- commandArgs(trailingOnly = TRUE)
+
+# 检查参数数量
+if (length(args) != 2) {
+  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)
+}
+
+# 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]
+
+# 检查输入文件是否存在
+if (!file.exists(input_csv)) {
+  stop("输入文件不存在，请检查路径是否正确。", call. = FALSE)
+}
+
+# 加载绘图数据
+data <- read.table(file = input_csv, header = TRUE, row.names = 1, sep = ',')
+
+# 查看数据
+head(data)
+
+# 转化matrix格式矩阵及数据归一化
+data <- as.matrix(data)
+cir1 <- t(scale(t(data)))
+
+# 处理 NA 值
+cir1[is.na(cir1)] <- 0
+
+# 查看归一化后的数据
+head(cir1)
+
+# 定义热图颜色梯度
+mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
+mycol1 <- colorRamp2(c(-2, 0, 2), c("#003399", "white", "#cccc00"))
+
+# 打开PDF设备
+pdf(output_pdf, width = 10, height = 8)
+
+# 默认参数绘制普通热图
+Heatmap(cir1, row_names_gp = gpar(fontsize = 6),
+        column_names_gp = gpar(fontsize = 8),
+        col = mycol,
+        name = "legend")
+
+# 计算数据大小范围
+range(cir1)
+
+# 绘制基础环形热图
+circos.heatmap(cir1, col = mycol)
+circos.clear()
+
+# 在circos.heatmap()中添加参数进行环形热图的调整和美化
+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()
+
+# 聚类树的调整和美化
+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()
+
+# 添加图例标签等
+lg <- Legend(title = "Exp", col_fun = mycol,
+             direction = c("vertical"))
+grid.draw(lg)
+
+# 添加列名
+circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
+  if (CELL_META$sector.numeric.index == 1) {
+    cn <- colnames(cir1)
+    n <- length(cn)
+    circos.text(rep(CELL_META$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()
+
+# 关闭PDF设备
+dev.off()
+
+message("热图已成功保存到: ", output_pdf)