2025-06-09
火山图（Volcano Plot）是单细胞转录组测序数据分析中常用的可视化工具，它通过将基因的差异表达程度（fold change，FC）和统计学显著性（p-value 或调整后的 p-value，如 FDR）相结合，直观地展示基因在不同组别或细胞类型下的差异表达情况。
相比于普通火山图，多组火山图可以展示更多分组或细胞类型，如下图所示，表示的是每个细胞类型中的上下调基因情况，和普通火山图一样，根据log2FC和矫正后P值进行绘制，红色散点表示上调基因，蓝色散点表示下调基因。
一般情况下，大家可能会画6张传统的火山图，用曼哈顿火山图一张就可以搞定！是不是很有用！是不是很想学！那我们现在就开始绘制！
第一步骤：准备数据
markers为组间比较结果的差异基因表格或findAllmarker结果的基因列表
markers = markers %>% filter(p_val < 0.05) %>% filter(abs(avg_log2FC) >= 0.25)
scRNA.markers = markers
scRNA.markers$label <- ifelse(scRNA.markers$avg_log2FC<0,"sigDown","sigUp")
topgene <- scRNA.markers %>%
group_by(celltype) %>%
top_n(n = 10, wt = avg_log2FC) %>%
bind_rows(group_by(scRNA.markers, celltype) %>%
top_n(n = 10, wt = -avg_log2FC))
dfbar = scRNA.markers %>%
group_by(celltype) %>%
summarise(low = round(min(avg_log2FC)-0.5),
up = round(max(avg_log2FC)+0.5))
得到如图所示数据：
第二步骤：绘制灰色背景柱和分组散点
p1 <- ggplot()+
geom_col(aes(x = celltype ,y = low),dfbar,
fill = "#dcdcdc",alpha = 0.6)+
geom_col(aes(x = celltype ,y = up),dfbar,
fill = "#dcdcdc",alpha = 0.6)+
geom_jitter(aes(x = celltype, y = avg_log2FC, color = label),scRNA.markers,
size = 1,alpha=0.5,position = position_jitter(seed = 1234,width =0.4))+
scale_color_manual(values = c("#0077c0","#c72d2e"))+
theme_classic()
第三步骤：添加分组颜色色块和标签
p2 <- p1 +
geom_tile(aes(x = ctys,y = 0),NULL,
height = 0.5,fill = mycol, show.legend = F,alpha = 0.5)+
geom_text(aes(x= ctys, y = 0, label = ctys),NULL,
size = 3,fontface = "bold")
第四步骤：添加基因标签
p3 <- p2 +
geom_text_repel(aes(x = celltype,y = avg_log2FC,label = do_label), scRNA.markers, position = position_jitter(width =0.4),size = 2,box.padding = unit(0.2, "lines"),point.padding = unit(0.3, "lines"),min.segment.length = 0,max.overlaps = 120,segment.size=0.5,segment.alpha = 0.7 )
第五步骤：调整图片标题和风格
p3 <- p3+
labs(x = "CellType",y = "log2FoldChange",
title = "Differential expression genes")+
theme(
plot.title = element_text(size = 14,color = "black",face = "bold"),
axis.title = element_text(size = 12,color = "black",face = "bold"),
axis.line.y = element_line(color = "black",linewidth = 0.8),
axis.line.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
panel.grid = element_blank(),
legend.position = c(0.98,0.96),
legend.background = element_blank(),
legend.title = element_blank(),
legend.direction = "vertical",
legend.justification = c(1,0),
legend.text = element_text(size = 12)
)+
guides(color = guide_legend(override.aes = list(size = 4)))
好看且内容丰富的多组火山图就完成啦！！
绘制图片或者复现代码过程中，如果老师遇到疑惑，欢迎拨打我们的热线电话或者联系我们的驻地销售。
