yongcaihuang-lab/Maize_Stem_Spatial_Project

1Violin_plot <- function(GeneID){2  3  # =======================================================4  # 1. 提取基因表达数据5  # =======================================================6  B73_Spot_Data <- Seurat::FetchData(B73, vars = c(GeneID, "annotation_final_detailed"), layer = "data")7  colnames(B73_Spot_Data) <- c("Value", "Tissue")8  B73_Spot_Data$Sample <- "B73"9  B73_Spot_Data$Barcode <- rownames(B73_Spot_Data)10  11  Teo_Spot_Data <- Seurat::FetchData(Ames21814, vars = c(GeneID, "annotation_final_detailed"), layer = "data")12  colnames(Teo_Spot_Data) <- c("Value", "Tissue")13  Teo_Spot_Data$Sample <- "Ames21814"14  Teo_Spot_Data$Barcode <- rownames(Teo_Spot_Data)15  16  All_Spots_Df <- rbind(B73_Spot_Data, Teo_Spot_Data)17  All_Spots_Df$Value <- as.numeric(All_Spots_Df$Value)18  19  # =======================================================20  # 2. 定义 Cell 风格的高级配色21  # =======================================================22  cell_colors <- c(23    "B73" = "#0072B5",       24    "Ames21814" = "#BC3C29"  25  )26  27  # =======================================================28  # 3. 绘制高级感小提琴图29  # =======================================================30  p_final <- ggplot(All_Spots_Df, aes(x = Tissue, y = Value, fill = Sample)) +31    32    # --- 1. 绘制小提琴图 ---33    geom_violin(34      position = position_dodge(width = 0.8),35      scale = "width",36      trim = TRUE,37      alpha = 0.95,        38      color = "#FAF9F6",   39      linewidth = 0.6,     40      width = 0.841    ) +42    43    # --- 2. 添加显著性检验 ---44    ggpubr::stat_compare_means( aes(group = Sample), 45                                method = "wilcox.test", 46                                label = "p.signif", 47                                vjust = 0.5, 48                                symnum.args = list( cutpoints = c(0, 1e-4, 1e-3, 1e-2, 5e-2, 1), 49                                                    symbols = c("****","***","**","*","ns") ) )+50    51    # --- 3. 应用自定义 Cell 配色 ---52    scale_fill_manual(values = cell_colors) +53    54    # --- 4. 主题设置 ---55    theme_bw() + 56    57    labs(58      y = "Expression Level", 59      x = NULL,60      caption = "**** p < 1e-4, *** p < 1e-3, ** p < 1e-2, * p < 5e-2,  ns p > 5e-2" 61    ) 62    63    theme(64      text = element_text(family = "serif"),65      plot.title = element_blank(),66      67      # 坐标轴文字68      axis.text.x = element_text(angle = 45, hjust = 1, size = 11, face = "bold", color = "black"),69      axis.text.y = element_text(size = 10, color = "black"),70      axis.title.y = element_text(size = 12, face = "bold", margin = margin(r = 10)),71      72      # ==========================================73      # 修改点：图例文字加粗、纯黑74      # ==========================================75      legend.position = "right",76      legend.title = element_blank(),77      legend.text = element_text(size = 11, face = "bold", color = "black"), 78      79      # 底部注释80      plot.caption = element_text(hjust = 0, size = 10, face = "italic", color = "black"),81      82      # 去掉网格线83      panel.grid.major = element_blank(),84      panel.grid.minor = element_blank(),85      86      # 去掉矩形框，只留 L 型坐标轴 87      panel.border = element_blank(),88      axis.line = element_line(color = "black", linewidth = 0.8),89      axis.ticks = element_line(color = "black", linewidth = 0.8)90    )91  92  return(p_final)93}