用ggplot2画火山图

用ggplot2画火山图看代码似乎还是很简单，但是真的来画了，细节还是蛮多的。

把代码写在这里，以便以后用。

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

library(ggplot2) library（Cairo） data <- read.delim("./data/g1_VS_g3.txt",header = T,sep="\t",na.strings = "") # 设置颜色域 data$threshold = as.factor(data$pvalues < 0.05 & abs(log2(data$foldchange)) >=1.5) Cairo(file="volcan_PNG_300_dpi.png",       type="png",       units="in",       bg="white",       width=8,       height=6,       pointsize=12,       dpi=300) ggplot(data=data,             aes(x=log2(foldchange), y =-log10(pvalues),                 colour=threshold)) +   geom_point(alpha=0.4, size=1.75) +   xlim(c(-4, 4)) +   xlab("log2 fold change") + ylab("-log10 p-value") +   ggtitle("Volcano picture of DEG")+   theme_gray() +   geom_vline(xintercept=c(-1.5,1.5),lty=4,col="grey",lwd=0.5)+ # 在x轴-1.5与1.5的位置画两根竖线   geom_hline(yintercept = -log10(0.05),lty=4,col="grey",lwd=0.5)+ 在p value 0.05的位置画一根横线   theme(legend.position="none") dev.off()

图1. volcano of DEGs

这只是一个粗略的图，要细致，还需要调整网格，坐标轴，颜色，字体大小，等等……

我们能不能将下调，上调的分别改变颜色体现呢？

那就来试试吧，思路其实就是颜色的映射到不同的 见前代码colour=threshold ，之前的设置只设定了2个水平，显著or不显著。那其实只要把显著与不显著改成上调、下调、无显著改变就可以了。见代码：

1	data$threshold <- as.factor(ifelse(data$pvalues < 0.05 & abs(log2(data$foldchange)) >=1.5,ifelse(log2(data$foldchange) > 1.5 ,'Up','Down'),'Not'))

建立好了分层，我们还需要做的一点是，分配颜色。

1	scale_color_manual(values=c("blue", "grey","red"))

这样就搞定了。但是，但是，强迫症估计还要加上图历，映射不同颜色是吧，呵呵。那就看下面的代码吧

1	theme(legend.position="right")

这样通过legend.position 指定显示的位置，或许你还想更改图例的标题，%……%……这需要你自己动手了，google or bing去寻求学习。

下面放出完整代码：

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70

library(ggplot2) library(ggthemes) library(Cairo) data <- read.delim("./data/g1_VS_g3.txt",header = T,sep="\t",na.strings = "") data$threshold <- as.factor(ifelse(data$pvalues < 0.05 & abs(log2(data$foldchange)) >=1.5,ifelse(log2(data$foldchange) > 1.5 ,'Up','Down'),'Not')) ##Construct the plot object # with legend Cairo(file="volcan_PNG_300_lengend_dpi.png",       type="png",       units="in",       bg="white",       width=5.5,       height=5,       pointsize=12,       dpi=300) ggplot(data=data,             aes(x=log2(foldchange), y =-log10(pvalues),                 colour=threshold,fill=threshold)) +   scale_color_manual(values=c("blue", "grey","red"))+   geom_point(alpha=0.4, size=1.2) +   xlim(c(-4, 4)) +   theme_bw(base_size = 12, base_family = "Times") +   geom_vline(xintercept=c(-1.5,1.5),lty=4,col="grey",lwd=0.6)+   geom_hline(yintercept = -log10(0.05),lty=4,col="grey",lwd=0.6)+   theme(legend.position="right",         panel.grid=element_blank(),         legend.title = element_blank(),         legend.text= element_text(face="bold", color="black",family = "Times", size=8),         plot.title = element_text(hjust = 0.5),         axis.text.x = element_text(face="bold", color="black", size=12),         axis.text.y = element_text(face="bold",  color="black", size=12),         axis.title.x = element_text(face="bold", color="black", size=12),         axis.title.y = element_text(face="bold",color="black", size=12))+   labs(x="log2 (fold change)",y="-log10 (p-value)",title="Volcano picture of DEG") dev.off() # without legend Cairo(file="volcan_PNG_300_dpi.png",       type="png",       units="in",       bg="white",       width=6,       height=5,       pointsize=12,       dpi=300) ggplot(data=data,        aes(x=log2(foldchange), y =-log10(pvalues),            colour=threshold,fill=threshold)) +   scale_color_manual(values=c("blue", "grey","red"))+   geom_point(alpha=0.4, size=1.2) +   xlim(c(-4, 4)) +   theme_bw(base_size = 12, base_family = "Times") +   geom_vline(xintercept=c(-1.5,1.5),lty=4,col="grey",lwd=0.6)+   geom_hline(yintercept = -log10(0.05),lty=4,col="grey",lwd=0.6)+   theme(legend.position="none",         panel.grid=element_blank(),         # legend.title = element_blank(),         # legend.text= element_text(face="bold", color="black",family = "Times", size=8),         plot.title = element_text(hjust = 0.5),         axis.text.x = element_text(face="bold", color="black", size=12),         axis.text.y = element_text(face="bold",  color="black", size=12),         axis.title.x = element_text(face="bold", color="black", size=12),         axis.title.y = element_text(face="bold",color="black", size=12))+   labs(x="log2 (fold change)",y="-log10 (p-value)",title="Volcano picture of DEG") dev.off()

 

图2. volcano of DEGs without legend

 

图3. volcano of DEGs with legend