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。
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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$foldchange)) >=1.5)
Cairo(file="volcan_PNG_300_dpi.png",
type="png",
units="in",
bg="white",
width=8,
height=6,
pointsize=12,
dpi=300)
ggplot(data=data,
aes(x=log2(foldchange), y =-log10(pvalues),
colour=threshold)) +
geom_point(alpha=0.4, size=1.75) +
xlim(c(-4, 4)) +
xlab("log2 fold change") + ylab("-log10 p-value") +
ggtitle("Volcano picture of DEG")+
theme_gray() +
geom_vline(xintercept=c(-1.5,1.5),lty=4,col="grey",lwd=0.5)+ # 在x轴-1.5与1.5的位置画两根竖线
geom_hline(yintercept = -log10(0.05),lty=4,col="grey",lwd=0.5)+ 在p value 0.05的位置画一根横线
theme(legend.position="none")
dev.off()
图1. volcano of DEGs
这只是一个粗略的图，要细致，还需要调整网格，坐标轴，颜色，字体大小，等等……
我们能不能将下调，上调的分别改变颜色体现呢？
那就来试试吧，思路其实就是颜色的映射到不同的 见前代码colour=threshold ，之前的设置只设定了2个水平，显著or不显著。那其实只要把显著与不显著改成上调、下调、无显著改变就可以了。见代码：
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data$threshold <- as.factor(ifelse(data$pvalues < 0.05 & abs(log2(data$foldchange)) >=1.5,ifelse(log2(data$foldchange) > 1.5 ,'Up','Down'),'Not'))
建立好了分层，我们还需要做的一点是，分配颜色。
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scale_color_manual(values=c("blue", "grey","red"))
这样就搞定了。但是，但是，强迫症估计还要加上图历，映射不同颜色是吧，呵呵。那就看下面的代码吧
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theme(legend.position="right")
这样通过legend.position 指定显示的位置，或许你还想更改图例的标题，%……%……这需要你自己动手了，google or bing去寻求学习。
下面放出完整代码：
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library(ggplot2)
library(ggthemes)
library(Cairo)
data <- read.delim("./data/g1_VS_g3.txt",header = T,sep="\t",na.strings = "")
data$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
