参考：
- Examples • ggrepel (slowkow.com)[1]
前言
上一讲我们提到了66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）[2]
可是，有的时候，并不是所有的text 文本，都可以非常理想的实现我们希望达到的效果。
这时候颜值高一些的ggrepel 就登场了：
代码语言：javascript复制library(ggrepel)
set.seed(42)
dat <- subset(mtcars, wt > 2.75 & wt < 3.45)
dat$car <- rownames(dat)
p <- ggplot(dat, aes(wt, mpg, label = car))
geom_point(color = "red")
p1 <- p geom_text() labs(title = "geom_text()")
p2 <- p geom_text_repel() labs(title = "geom_text_repel()")
gridExtra::grid.arrange(p1, p2, ncol = 2)
包的功能如其名字，repel，就是让标记被原本的点推开~
美化作图：以火山图为例
如下效果：
老规矩先加载包：
代码语言：javascript复制my_packages<- c("maftools", "data.table",
"RColorBrewer", "paletteer", "ggplot2",
"ggpubr", "tidyverse", "REdaS", "ggrepel")
tmp <- sapply(my_packages, function(x) library(x, character.only = T)); rm(tmp, my_packages)
接着就是完整代码了：
代码语言：javascript复制# 2. ggrepel ----
set.seed(1234)
DEG <- data.frame(
genes = paste0("gene", 1:100),
fold_change = round(runif(100, -10, 10), 2),
P_value = runif(100, 0.001, 0.1)
)
DEG$group <- ifelse((DEG$P_value > 0.05) | (abs(DEG$fold_change) < 2) , "no-Significant",
ifelse(DEG$fold_change > 2, "increase", "decrease"))
DEG$group <- factor(DEG$group, levels = c("decrease", "no-Significant",
"increase"))
sig_DEG <- DEG[!DEG$group %in% "no-Significant",]
head_genes <- head(sig_DEG[order(abs(sig_DEG$fold_change), decreasing = T),]$genes, 15)
for_label <- DEG[DEG$genes %in% head_genes,]
(p <- ggplot(data = DEG,
aes(x = fold_change,
y = -log10(P_value)))
geom_point(size=3.5, alpha = 0.6,
aes(color = group))
theme_bw() theme(
axis.title = element_text(size = 14, face = "bold"),
axis.text = element_text(size = 14),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12))
ylab("-log10(Pvalue)")
scale_color_manual(values = c("blue", "grey", "red"))
geom_hline(yintercept = -log10(0.05),lty=4,col="black",lwd=0.8)
geom_vline(xintercept = c(-2, 2),lty=4,col="black",lwd=0.8)
geom_label_repel(
data = for_label,
aes(label = genes),
alpha = 0.7,
max.overlaps = 15
)
)
我们可以对比一下geom_label:
关键就是geom_text_repel 这个函数啦~
一些参数与操作
操作
隐藏某些labels
代码语言：javascript复制dat2 <- subset(mtcars, wt > 3 & wt < 4)
# Hide all of the text labels.
dat2$car <- ""
# Let's just label these items.
ix_label <- c(2, 3, 14)
dat2$car[ix_label] <- rownames(dat2)[ix_label]
ggplot(dat2, aes(wt, mpg, label = car))
geom_text_repel()
geom_point(color = ifelse(dat2$car == "", "grey50", "red"))
对于大量散点图就可以非常实用的实现显示关键点了：
代码语言：javascript复制set.seed(42)
dat3 <- rbind(
data.frame(
wt = rnorm(n = 10000, mean = 3),
mpg = rnorm(n = 10000, mean = 19),
car = ""
),
dat2[,c("wt", "mpg", "car")]
)
ggplot(dat3, aes(wt, mpg, label = car))
geom_point(data = dat3[dat3$car == "",], color = "grey50")
geom_text_repel(box.padding = 0.5, max.overlaps = Inf)
geom_point(data = dat3[dat3$car != "",], color = "red")
标记们，你们可别聚众打架啊
代码语言：javascript复制set.seed(42)
n <- 15
dat4 <- data.frame(
x = rep(1, length.out = n),
y = rep(1, length.out = n),
label = letters[1:n]
)
# Set it globally:
options(ggrepel.max.overlaps = Inf)
p1 <- ggplot(dat4, aes(x, y, label = label))
geom_point()
geom_label_repel(box.padding = 0.5, max.overlaps = 10)
labs(title = "max.overlaps = 10 (default)")
p2 <- ggplot(dat4, aes(x, y, label = label))
geom_point()
geom_label_repel(box.padding = 0.5)
labs(title = "max.overlaps = Inf")
gridExtra::grid.arrange(p1, p2, ncol = 2)
自行感受啦~
把标记往左往右推
代码语言：javascript复制set.seed(42)
d <- data.frame(
x1 = 1,
y1 = rnorm(10),
x2 = 2,
y2 = rnorm(10),
lab = state.name[1:10]
)
p <- ggplot(d, aes(x1, y1, xend = x2, yend = y2, label = lab, col = lab))
geom_segment(size = 1)
guides(color = "none")
theme(axis.title.x = element_blank())
geom_text_repel(
nudge_x = -0.2, direction = "y", hjust = "right"
)
geom_text_repel(
aes(x2, y2), nudge_x = 0.1, direction = "y", hjust = "left"
)
p scale_x_continuous(
breaks = 1:2, labels = c("Dimension 1", "Dimension 2"),
expand = expansion(mult = 0.5)
)
主要和nudge_* 参数有关。
永远有线
代码语言：javascript复制p <- ggplot(dat, aes(wt, mpg, label = car))
geom_point(color = "red")
p1 <- p
geom_text_repel(min.segment.length = 0, seed = 42, box.padding = 0.5)
labs(title = "min.segment.length = 0")
p2 <- p
geom_text_repel(min.segment.length = Inf, seed = 42, box.padding = 0.5)
labs(title = "min.segment.length = Inf")
gridExtra::grid.arrange(p1, p2, ncol = 2)
我们还可以给线段拐个歪~
代码语言：javascript复制set.seed(42)
ggplot(dat, aes(wt, mpg, label = car))
geom_point(color = "red")
geom_text_repel(
nudge_x = .15,
box.padding = 0.5,
nudge_y = 1,
segment.curvature = -0.1,
segment.ncp = 3,
segment.angle = 20
)
永远靠边站
hjust 参数，0 是靠右，0.5 居中，1 是靠左：
set.seed(42)
p <- ggplot(mtcars, aes(y = wt, x = 1, label = rownames(mtcars)))
geom_point(color = "red")
ylim(1, 5.5)
theme(
axis.line.x = element_blank(),
axis.ticks.x = element_blank(),
axis.text.x = element_blank(),
axis.title.x = element_blank()
)
p1 <- p
xlim(1, 1.375)
geom_text_repel(
force = 0.5,
nudge_x = 0.15,
direction = "y",
hjust = 0,
segment.size = 0.2
)
ggtitle("hjust = 0")
p2 <- p
xlim(1, 1.375)
geom_text_repel(
force = 0.5,
nudge_x = 0.2,
direction = "y",
hjust = 0.5,
segment.size = 0.2
)
ggtitle("hjust = 0.5 (default)")
p3 <- p
xlim(0.25, 1)
scale_y_continuous(position = "right")
geom_text_repel(
force = 0.5,
nudge_x = -0.25,
direction = "y",
hjust = 1,
segment.size = 0.2
)
ggtitle("hjust = 1")
gridExtra::grid.arrange(p1, p2, p3, ncol = 3)
柱状图标记文本的新思路
我先前写过：66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）[3]
这样有个小箭头，好像也还不错~
p <- ggplot(mtcars, aes(factor(cyl), mpg))
stat_summary(
fill = "gray90",
colour = "black",
fun = "mean",
geom = "col"
)
p1 <- p stat_summary(
aes(label = round(stat(y))),
fun = "mean",
geom = "text_repel",
min.segment.length = 0, # always draw segments
position = position_nudge(y = -2)
)
labs(title = "position_nudge()")
p2 <- p stat_summary(
aes(label = round(stat(y))),
fun = "mean",
geom = "text_repel",
min.segment.length = 0, # always draw segments
position = position_nudge_repel(y = -2)
)
labs(title = "position_nudge_repel()")
gridExtra::grid.arrange(p1, p2, ncol = 2)
参数
这里我都是节选的官方说明文档中的介绍：Examples • ggrepel (slowkow.com)[4]
如果需要了解更多实例，参见上面的文档。
这里复习一下参数：
代码语言：javascript复制nudge_x：调整标签x轴位置
nudge_y：同上
bg.color = "grey30", # shadow color
bg.r = 0.15 # shadow radius
hjust ：调整文本的位置
max.overlaps = Inf # 永远显示线段
segment.size = 0.1
segment.linetype = 6
segment.curvature = -0.1
# 改善一下你的线段的风格
direction # x轴放置还是y 轴放置
再来改善一下火山图
灵感和代码参加：RNAseqStat/enhance_volcano.R at master · xiayh17/RNAseqStat (github.com)[5]
代码语言：javascript复制(p <- ggplot(data = DEG,
aes(x = fold_change,
y = -log10(P_value)))
geom_point(size=3.5, alpha = 0.6,
aes(color = group))
geom_point(size = 3, shape = 1, data = for_label)
theme_bw() theme(
axis.title = element_text(size = 14, face = "bold"),
axis.text = element_text(size = 14),
legend.title = element_text(size = 14),
legend.text = element_text(size = 12))
scale_x_continuous(expand = c(0.15, 0.15))
ylab("-log10(Pvalue)")
scale_color_manual(values = c("blue", "grey", "red"))
geom_hline(yintercept = -log10(0.05),lty=4,col="black",lwd=0.8)
geom_vline(xintercept = c(-2, 2),lty=4,col="black",lwd=0.8)
geom_text_repel(
size = 4,
data = for_label[which(for_label$fold_change < 0),],
aes(label = genes),
nudge_y = -0.2,
direction = "y",
hjust = 1,
segment.size = 0.1,
segment.linetype = 6,
segment.curvature = -0.1,
max.overlaps = 10,
max.iter = 1000000,
max.time = 10,
nudge_x = for_label[which(for_label$fold_change < 0),]$fold_change 1.1*min(for_label$fold_change),
min.segment.length = 0,
bg.color = "#e0e0e0", # shadow color
bg.r = 0.15 # shadow radius
)
geom_text_repel(
size = 4,
data = for_label[which(for_label$fold_change > 0),],
aes(label = genes),
nudge_y = -0.2, # move
direction = "y",
hjust = 0,
segment.size = 0.1,
segment.linetype = 6,
segment.curvature = -0.1,
max.overlaps = 10, # never overlaps
max.iter = 1000000,
max.time = 10, # DO NOT show too much overlaps
nudge_x = for_label[which(for_label$fold_change > 0),]$fold_change 1.1*max(for_label$fold_change),
# right move right
min.segment.length = 0, # always lines
bg.color = "#e0e0e0", # shadow color
bg.r = 0.15 # shadow radius
)
)
你喜欢吗？
参考资料
[1]Examples • ggrepel (slowkow.com): https://ggrepel.slowkow.com/articles/examples.html
[2]66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）: 66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）.md
[3]66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）: 66-R可视化10-自由的在ggplot上添加文本（柱状图加计数）.md
[4]Examples • ggrepel (slowkow.com): https://ggrepel.slowkow.com/articles/examples.html#examples-1
[5]RNAseqStat/enhance_volcano.R at master · xiayh17/RNAseqStat (github.com): https://github.com/xiayh17/RNAseqStat/blob/master/R/enhance_volcano.R
