繪圖技巧 - 火山圖 | volcano plot

 

標簽：RNA-seq；基因表達

 

一個非常常見的圖種，用於表示兩組數據基因表達差異的圖，通常橫縱坐標分別為 Log2FC 和 P-value。

 

畫出來並不難

美化稍微有點難度：標注重要的點，點的顏色、形狀、圖層順序。

 

基本數據准備：

1. 帶log2FC和P-value的dataframe
2. 需要標注的數據點

 

代碼：

# prepare main dataset
data.df <- c1.markers.DESeq2
## API
data.df$log2FC <- data.df$avg_logFC
data.df$p_value <- data.df$p_val
data.df$gene <- rownames(data.df)
## color
data.df$color <- "black"
data.df[data.df$gene %in% oxidation.go.genes,]$color <- "red"

# prepare annotation data point
mark.df <- subset(data.df, gene %in% oxidation.go.genes)

library("ggrepel")
options(repr.plot.width=6, repr.plot.height=6)
ggplot(data.df, aes(x=log2FC, y=-log10(p_value))) +
    geom_hline(aes(yintercept=1), colour="grey50", linetype="dashed", size=0.2) + 
    #geom_vline(aes(xintercept=0.5), colour="red", linetype="dashed", size=0.2) + 
    geom_vline(aes(xintercept=0), colour="grey50", linetype="dashed", size=0.2) + 
    geom_point(aes(color=color), stroke = 0.3, size=1) + # 
    scale_color_manual(values=c("black", "red")) +
    labs(x = "Log2 fold change\n",y = "-Log10(P-value)", title = "") +
    theme_bw() +
    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
          panel.border = element_rect(size=0.8, colour = "black")) +
    theme(axis.title =element_text(size = 16),axis.text =element_text(size = 10, color = "black"),
          plot.title =element_text(hjust = 0.5, size = 16)) +
    #scale_x_continuous(position="bottom", breaks = seq(-10, 10, by = 2), limits=c(-10, 10)) +
    #scale_y_continuous(position="left", breaks = seq(-10, 10, by = 2), limits=c(-10, 10)) +
    theme(legend.title=element_blank(), legend.position = "none") +
    # theme(legend.title=element_blank(), legend.key.size = unit(0.8, 'lines')) +
    geom_text_repel(data=mark.df, aes(label=gene), color="red", size=3.8, fontface="italic", 
                    arrow = arrow(ends="first", length = unit(0.01, "npc")), box.padding = 0.2, 
                    point.padding = 0.3, segment.color = 'black', segment.size = 0.3, force = 1, max.iter = 3e3) #+
    #scale_fill_manual(values=c("blue", "red"))

 

成圖：

 

 

不是很美觀，以后多看看發在CNS上的火山圖，模仿一下。

 

　　

 

 

參考：

Ezh2項目文章的圖：mouse/singleCell/case/Kif7_ENCC/Kif7-integration/Ezh2_analysis.ipynb