火山图代码

# 安装所需的包，如果已经安装可以跳过这一步
install.packages("ggplot2")
install.packages("ggrepel")

# 加载包
library(ggplot2)
library(ggrepel)

# 假设你的数据框叫做 data
# data <- read.csv("你的数据文件.csv")  # 如果你的数据在CSV文件中

# 计算-log10(P值)
data$neg_log10_pvalue <- -log10(data$P.Value)

# 定义显著性阈值
pvalue_thresh <- 0.05
logfc_thresh <- 1

# 定义一个新列来表示显著性（你可以根据需要自定义这些颜色）
cluster5.markers$threshold <- with(cluster5.markers, 
                                   factor(ifelse(p_val < pvalue_thresh & abs(avg_log2FC) > logfc_thresh,
                                                 ifelse(avg_log2FC >= logfc_thresh, "up", "down"),
                                                 "not_significant"),
                                          levels = c('up', 'down', 'not_significant')))

# 绘制火山图
volcano_plot <- ggplot(cluster5.markers, aes(x = avg_log2FC, y = neg_log10_pvalue, color = threshold)) +
  geom_point(size = 1.5, alpha = 0.6) +  # 调整点的大小和透明度
 
  geom_vline(xintercept = c(logfc_thresh,-logfc_thresh), linetype = "dashed", color = "black")+
  geom_hline(yintercept = -log10(pvalue_thresh), linetype = "dashed", color = "black") +  # 添加横线  
  labs(x = "Log2 Fold Change", y = "neg_log10_pvalue", title = "Volcano Plot") +  # 添加坐标轴标签和标题
  scale_color_manual(values = c(not_significant="grey", up = "red", down = "green"))+  # 定义颜色  
  theme_minimal()  # 使用简洁的主题 

# 打印火山图
print(volcano_plot)

# 如果你想要为显著的基因添加标签，上调基因前五个
top_up_genes <- cluster5.markers[cluster5.markers$avg_log2FC > logfc_thresh & cluster5.markers$p_val < pvalue_thresh, ]
top_up_genes <- top_up_genes[order(top_up_genes$p_val), ]
top_up_genes <- top_up_genes[1:5, ]

# 筛选下调最显著的五个基因
top_down_genes <- cluster5.markers[cluster5.markers$avg_log2FC < -logfc_thresh & cluster5.markers$p_val < pvalue_thresh, ]
top_down_genes <- top_down_genes[order(top_down_genes$p_val), ]
top_down_genes <- top_down_genes[1:5, ]
###将筛选出的基因放回之前的数据集
cluster5.markers$jiyin[which(cluster5.markers$label == "RPS27")] <- "RPS27"
cluster5.markers$jiyin[which(cluster5.markers$label == "RPL13A")] <- "RPL13A"
cluster5.markers$jiyin[which(cluster5.markers$label == "RPL13")] <- "RPL13"
cluster5.markers$jiyin[which(cluster5.markers$label == "RPS18")] <- "RPS18"
cluster5.markers$jiyin[which(cluster5.markers$label == "RPL3")] <- "RPL3"

# 绘制带有基因标签的火山图
volcano_plot_with_labels <- volcano_plot + geom_text_repel(aes(label = jiyin), size = 3, point.padding = 0.5, box.padding = 0.5)

# 打印带有基因标签的火山图
print(volcano_plot_with_labels)