84 lines
2.4 KiB
R
84 lines
2.4 KiB
R
# 加载所需的包
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suppressPackageStartupMessages(library(circlize))
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suppressPackageStartupMessages(library(RColorBrewer))
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suppressPackageStartupMessages(library(ComplexHeatmap))
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suppressPackageStartupMessages(library(dendextend))
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# 获取命令行参数
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args <- commandArgs(trailingOnly = TRUE)
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# 检查参数数量
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if (length(args) != 2) {
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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)
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}
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# 获取输入CSV文件路径和输出PDF文件路径
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input_csv <- args[1]
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output_pdf <- args[2]
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# 检查输入文件是否存在
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if (!file.exists(input_csv)) {
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stop("输入文件不存在。请检查文件路径。", call. = FALSE)
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}
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# 函数加载和预处理数据
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load_and_preprocess_data <- function(file_path) {
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data <- read.table(file = file_path, header = TRUE, row.names = 1, sep = ',')
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data_matrix <- as.matrix(data)
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normalized_data <- t(scale(t(data_matrix)))
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normalized_data[is.na(normalized_data)] <- 0
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return(normalized_data)
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}
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# 加载和预处理数据
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cir1 <- load_and_preprocess_data(input_csv)
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# 打印数据维度和头部
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print(dim(cir1))
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print(head(cir1))
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# 定义颜色梯度
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mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
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# 打开PDF设备，设置宽度和高度相等
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pdf(output_pdf, width = 8, height = 8)
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# 设置绘图参数
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circos.par(gap.after = c(30))
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# 绘制调整后的圆形热图
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circos.heatmap(cir1,
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col = mycol,
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dend.side = "inside",
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rownames.side = "outside",
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rownames.col = "black",
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rownames.cex = 1.3,
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track.height = 0.35, # 增加轨道高度
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cluster = TRUE,
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dend.track.height = 0.18,
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dend.callback = function(dend, m, si) {
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color_branches(dend, k = 15, col = 1:15)
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})
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# 添加列名
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circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
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if (CELL_META$sector.numeric.index == 1) {
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cn <- colnames(cir1)
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n <- length(cn)
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circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"),
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1:n + 2.5,
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cn, cex = 1.0, adj = c(0, 0.5), facing = "inside") # 将 cex 从 0.6 改为 1.0
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}
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}, bg.border = NA)
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# 添加图例
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lg <- Legend(title = "Exp", col_fun = mycol, direction = "vertical")
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grid.draw(lg)
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# 清除圆形图
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circos.clear()
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# 关闭PDF设备
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dev.off()
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message(output_pdf) |