ggplot2: 小提琴图

用ggplot2绘制小提琴图

1. 绘制基础小提琴图

ggplot(data=, aes(x=, y=))+geom_violin(aes(fill=))
ggplot()+geom_violin(data=, aes(x=, y=, fill=))

> ff <- c(1:12, rnorm(8,7,1), c(8,3,4,5,7,1,2,3), c(9,0,3,7,2,67,44))
> ff <- c(ff, sample(ff, 27))
> ff <- c(ff, sample(ff, 32))
> 
> kk <- as.data.frame(list(sample(rep(1:5,100),length(ff)), ff))
> kk[,1] <- as.factor(kk[,1])
> kk[,2] <- abs(kk[,2])
> 
> colnames(kk) <- c("aa","bb")
> 
> head(kk, 10)
   aa bb
1   2  1
2   4  2
3   2  3
4   1  4
5   1  5
6   5  6
7   3  7
8   4  8
9   3  9
10  3 10
> kk[,1]
 [1] 2 4 2 1 1 5 3 4 3 3 3 1 4 1 1 1 2 5 4 2 4 4 5 2 5 4 3 2 2 4 4 5 3 3 4 3 4 4 2 4 3 2 5 1 1 5 3 1 5 2 3 3 4 4 4 4 1
[58] 5 4 2 5 4 5 5 5 4 3 4 4 2 5 5 1 1 1 5 3 4 1 5 5 3 5 4 1 1 3 1 2 3 5 2 2 5
Levels: 1 2 3 4 5
> 
> ggplot()+geom_violin(data=kk, aes(x=aa, y=bb, fill=aa))

图片.png

2. 旋转小提琴图

ggplot()+geom_violin(data=, aes(x=, y=, fill=))+coord_flip()

3. 在小提琴图中添加四分位图

ggplot()+geom_violin(data=, aes(x=, y=))+geom_boxplot(data=, aes(x=, y=), width=)
ggplot()+geom_violin(data=, aes(x=, y=))+geom_boxplot(data=, aes(x=, y=), width=, position = position_dodge())

其实就是小提琴图和箱线图的联用，并要主要控制箱线图的宽度

4. 添加中位数点和SD bar

require(hmisc)

ggplot(kk, aes(x = cluster, y = nCount_RNA)) + geom_violin(aes(fill=cluster)) + scale_y_log10()+stat_summary(fun.data = "mean_sdl", fun.args = list(mult = 1), geom = "pointrange", color = "white", size=1) + theme_cowplot()

list(mult = 1) : SD bar 为 1 SD
绘制出的图像，点为平均数，bar为 SD

image.png