火山图绘制

纳入数据

差异分析的数据
保证差异分析的数据包含p值，foldchange数据，以及根据前两者区分上下调基因的分类

导入基因

set.seed(123)
logFC <- rnorm(100, mean=0, sd=1)
pvalue <- runif(100, 0, 0.05)
gene_names <- paste("Gene", 1:100, sep="")
data <- data.frame(logFC=logFC, pvalue=pvalue, gene_names=gene_names)

对基因进行上下调分类

data$group <- ifelse(data$pvalue > 0.05, "NS", 
                            ifelse(data$pvalue < 0.05 & data$logFC > 0.7, "Up", 
                                   ifelse(data$pvalue < 0.05 & data$logFC < -0.7, "Down", "NS")))

绘制图形

初步绘制

ggplot(data, aes(x=logFC, y=-log10(PValue))) +
  geom_point(aes(color=group, size=abs(logFC)),  alpha=0.8) +
  labs(title="Volcano Plot", x="log2 Fold Change", y="-log10(p-value)") +
  geom_hline(yintercept=-log10(0.05), linetype="dashed", color="black") +
  geom_vline(xintercept=c(-0.7, 0.7), linetype="dashed", color="black") +
  scale_size(range = c(0.5, 3)) + 
  guides(size = guide_legend(override.aes = list(alpha = 1)))+
  theme_bw()

添加注释

sig_genes <- subset(data, pvalue < 0.01 & abs(logFC) > 1)

ggplot(data, aes(x=logFC, y=-log10(pvalue))) +
  geom_point(aes(color=pvalue), alpha=0.8) +
  scale_color_gradient(low="black", high="red") +
  labs(title="Volcano Plot", x="log2 Fold Change", y="-log10(p-value)") +
  annotate("text", x=sig_genes$logFC, y=-log10(sig_genes$pvalue),
           label=sig_genes$gene_names, size=3, color="blue")