「编程虚拟器官」R包OrgHeatmap自定义器官系统映射

library(OrgHeatmap)# 加载包内置的示例数据集data_path <- system.file("extdata",                          "exampledata.Rdata",                          package = "OrgHeatmap")load(data_path)# 查看数据集的结构head(example_Data3)# organ value# 10   lymph_nodes 0.029# 9           lung 0.041# 5         uterus 0.026# 17 adrenal_gland 0.014# 25        tongue 0.038# 18       stomach 0.050

# 使用默认设置创建器官基础可视化result <- OrgHeatmap(data = example_Data3)print(result$plot)# 直接用ggsave保存plot对象为PDFggsave(  filename = "basic_human_organ_ggsave.pdf",  plot = result$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")

# 可视化小鼠消化系统mouse_result <- OrgHeatmap(  data = example_Data1,  species = "mouse",  system = "digestive",  palette = "PuBu",  title = "Mouse Digestive System")print(mouse_result$plot)# 直接用ggsave保存plot对象为PDFggsave(  filename = "mouse_organ_ggsave.pdf",  plot = mouse_result$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")

# 聚焦特定器官系统circulatory_plot <- OrgHeatmap(  data = example_Data3,  system = "circulatory",  # 循环系统  title = "Circulatory System Data",  showall = TRUE  # 显示所有器官轮廓作为背景参考)# 打印图表print(circulatory_plot$plot)# 用ggsave保存为PDFggsave(  filename = "Circulatory_System_Data.pdf",  plot = circulatory_plot$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")

respiratory_plot <- OrgHeatmap(  data = example_Data3,  system = "respiratory",  # 呼吸系统  palette = "PuBuGn",           # RColorBrewer调色板名称  reverse_palette = TRUE,       # 反转调色板颜色顺序  color_mid = "#87CEEB",        # 自定义中间色  organbar = TRUE,              # 显示器官对应的柱状图  organbar_title = "Mean Value",# 柱状图标题  title = "Respiratory System (PuBuGn Palette)")# 打印图表print(respiratory_plot$plot)# 保存为PDFggsave(  filename = "Respiratory_System_PuBuGn_Palette.pdf",  plot = respiratory_plot$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")

custom_plot <- OrgHeatmap(  data = example_Data3,  color_low = "#F7FBFF",        # 低值对应浅蓝  color_high = "#08306B",       # 高值对应深蓝  color_mid = "#6BAED6",        # 中值对应中等蓝色  organbar_low = "#FFF7BC",     # 柱状图低值对应浅黄  organbar_high = "#D95F0E",    # 柱状图高值对应深橙  title = "Custom Color Gradient")# 打印图表print(custom_plot$plot)# 保存为PDFggsave(  filename = "Custom_Color_Gradient.pdf",  plot = custom_plot$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")  

# 扩展默认器官系统映射（新增前列腺相关器官系统分类）prostate_organ_systems <- rbind(  human_organ_systems,  # 包内置的人类器官系统默认映射  data.frame(    organ = c("prostate", "bone", "lymph_node", "adrenal_gland"),    system = c("reproductive", "musculoskeletal", "lymphatic", "endocrine"),    stringsAsFactors = FALSE  ))extended_plot <- OrgHeatmap(  data = example_Data3,  organ_system_map = prostate_organ_systems,  # 应用扩展后的器官系统映射  system = "reproductive",                    # 生殖系统（含新增前列腺）  title = "Extended Organ System Mapping")# 打印图表print(extended_plot$plot)# 保存为PDFggsave(  filename = "Extended_Organ_System_Mapping.pdf",  plot = extended_plot$plot,  width = 7,  height = 7,  device = "pdf",  bg = "white")

# result <- OrgHeatmap(  data = example_Data3,  system = "circulatory",  save_plot = TRUE,  plot_path = file.path(getwd(), "circulatory_system.pdf"),  plot_width = 7,  plot_height = 7,    # plot_dpi = 600,  plot_device = "pdf",  save_clean_data = TRUE,  clean_data_path = file.path(getwd(), "cleaned_data.rds"))

# 访问返回结果的所有组成部分print(result$plot)           # ggplot2 绘图对象（生成的可视化图表）head(result$clean_data)      # 清洗后的数据集（展示前6行数据）result$system_used          # 用于数据筛选的器官系统（本次绘图所用）result$mapped_organs        # 标准化后的器官名称（已完成名称映射处理）result$missing_organs       # 缺少坐标信息的器官（无法进行可视化绘图）result$total_value          # 所有数据值的总和（对应绘图数据的总体统计值）