yongcaihuang-lab/Maize_Stem_Spatial_Project

1All_Spatial_plot <- function(GeneID){2  3  SpatialPlot_Function <- function(Sample, ID, titleID, limits = NULL) {4    5    # =======================================================6    # 1. 自动匹配样本名称逻辑7    # =======================================================8    current_ident <- as.character(unique(Sample$orig.ident))9    10    name_map <- c(11      "B73_1" = "B73-1",12      "B73_2" = "B73-2",13      "Ames21814_1" = "Ames21814-1",14      "Ames21814_2" = "Ames21814-2"15    )16    17    final_title <- name_map[current_ident]18    if (is.na(final_title)) final_title <- current_ident19    20    # =======================================================21    # 2. 基础绘图 (使用 suppressMessages 屏蔽内置 scale 警告)22    # =======================================================23    SFP <- suppressMessages({24      Seurat::SpatialFeaturePlot(25        Sample,26        features = ID,27        crop = TRUE,28        keep.scale = "feature",29        pt.size.factor = 2.1,30        image.alpha = 1,31        alpha = c(0.6, 1),32        stroke = NA,33        shape = 2134      ) + 35        # =======================================================36      # 3. 设置标题37      # =======================================================38      labs(title = final_title) + 39        40        # =======================================================41      # 4. 颜色与刻度42      # =======================================================43      scale_fill_gradient(44        low = "white",45        high = "darkred",46        limits = limits,47        oob = scales::squish,48        na.value = "lightgrey",49        guide = guide_colourbar(frame.linewidth = 1, ticks.linewidth = 0.5)50      ) +51        # =======================================================52      # 5. 主题设置53      # =======================================================54      theme(55        text = element_text(family = "serif"),56        plot.title = element_text(size = 16, hjust = 0.5, color = "black", family = "serif", face = "bold"),57        legend.position = "right", # 图例位置58        legend.title = element_blank(),59        plot.background = element_rect(fill = "transparent", color = NA),60        panel.background = element_rect(fill = "transparent", color = NA),61        panel.grid.major = element_blank(),62        panel.grid.minor = element_blank(),63        legend.background = element_rect(fill = "transparent", color = NA),64        legend.key = element_rect(fill = "transparent", color = NA)65      )66    })67    68    return(SFP)69  }70  71  # 提取数据时加入 na.rm 防止意外报错72  all_vals <- c(73    Seurat::FetchData(B73_1, vars = GeneID)[,1],74    Seurat::FetchData(B73_2, vars = GeneID)[,1],75    Seurat::FetchData(Ames21814_1, vars = GeneID)[,1],76    Seurat::FetchData(Ames21814_2, vars = GeneID)[,1]77  )78  79  # 设定统一范围80  global_limits <- c(0, max(all_vals, na.rm = TRUE))81  82  # 画图（传入 limits）83  p_B3 <- SpatialPlot_Function(B73_1, GeneID, GeneID, limits = global_limits)84  p_B7 <- SpatialPlot_Function(B73_2, GeneID, GeneID, limits = global_limits)85  p_T1 <- SpatialPlot_Function(Ames21814_1, GeneID, GeneID, limits = global_limits)86  p_T3 <- SpatialPlot_Function(Ames21814_2, GeneID, GeneID, limits = global_limits)87  88  # =======================================================89  # 核心修改：拼图并合并刻度90  # =======================================================91  # 使用 patchwork 的语法： (上排) / (下排)92  # guides = "collect" 会自动提取所有相同的图例，并只保留一个93  Spatial_plot <- (p_B3 + p_B7) / (p_T1 + p_T3) + 94    patchwork::plot_layout(guides = "collect")95  96  return(Spatial_plot)97}