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2025-01-11 21:47:31 +08:00 · 2025-01-11 21:47:31 +08:00 · d3a9e4f691
commit d3a9e4f691
parent d0e9435465
1 changed files with 100 additions and 0 deletions
--- a/main.R
+++ b/main.R
@ -0,0 +1,100 @@
+# 列出所需的包
+packages <- c("ComplexHeatmap", "circlize", "RColorBrewer", "dendextend", "dendsort", "gridBase")
+
+# 检查并安装缺失的包
+install_if_missing <- function(pkg) {
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    if (pkg == "ComplexHeatmap") {
+      if (!requireNamespace("BiocManager", quietly = TRUE)) {
+        install.packages("BiocManager")
+      }
+      BiocManager::install("ComplexHeatmap")
+    } else {
+      install.packages(pkg, dependencies = TRUE)
+    }
+  }
+}
+
+# 应用函数到每个包
+sapply(packages, install_if_missing)
+
+# 加载所有包
+lapply(packages, library, character.only = TRUE)
+
+# 加载绘图数据
+data <- read.table(file = 'E:/hui.zhang/Drawpic/1.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"))
+
+# 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()