Question

我有这行代码：

plot(gene_list$logFC, -log10(gene_list$P.Value),xlim=c(-10, 10), ylim=c(0, 15),xlab="log2 fold change", ylab="-log10 p-value")

导致火山阴谋;但是我想找到一种方法，我可以用红色点＆gt; log（2）和

编辑：好的，作为一个例子，我试图做以下事情来获得火山阴谋：

install.packages("ggplot2")

然后

gene_list <- read.table("/Users/Javi/Desktop/gene_list.csv", header=T, sep=",")

require(ggplot2)
##Highlight genes that have an absolute fold change > 2 and a p-value <    0.05
gene_list$threshold = as.factor(abs(gene_list$logFC) > 2 & gene_list$P.Value < 0.05)

构造绘图对象

g = ggplot(data=gene_list, aes(x=logFC, y=-log10(P.Value),  colour=my_palette)) +
geom_point(alpha=0.4, size=5) +
theme(legend.position = "none") +
xlim(c(-10, 10)) + ylim(c(0, 15)) +
xlab("log2 fold change") + ylab("-log10 p-value")

我想要做的是为logFC值着色＆gt; 2和蓝色的logFC值＆lt; -2

Answer 1

您需要添加一个报告标签的阈值列 logFC值＆gt; 2，logFC值＆lt; -2，和之间的值：

mydata<-mydata%>%mutate(threshold = ifelse(logFC >= 2,"A", ifelse(logFC<=-2 , "B", "C")))

接下来，您将编写火山图并按geom_point和scale_colour_manual指定颜色。作为logFC＆lt; = - 2的标签的B是蓝色

ggplot(mydata, aes(x=logFC, y=log10)) +
geom_point(aes(colour = threshold), size=2.5) +
scale_colour_manual(values = c("A"= "yellow", "B"="blue",  "C"= "black"))

Answer 2

您需要使用col参数，类似的应该这样做：

# first set up the plot
plot(gene_list$logFC, -log10(gene_list$P.Value),
     xlim=c(-10, 10), ylim=c(0, 15),
     xlab="log2 fold change", ylab="-log10 p-value",
     type="n")
# then add the points
sel <- which(gene_list$logFD<=log(2)) # or whatever you want to use
points(gene_list[sel,"logFC"], -log10(gene_list[sel,"P.value"]),col="black")
sel <- which(gene_list$logFD>log(2)) # or whatever you want to use
points(gene_list[sel,"logFC"], -log10(gene_list[sel,"P.value"]),col="red")

R

构造绘图对象

2 个答案: