引言
jjAnno 是我三年前写的一个简单的工具，来给 ggplot 周围添加不同的注释图形。本质上是使用 annotation_custom 来实现的。最近 ggplot 4.0.0 版本更新了，可能再使用 jjAnno 会报错。比如 生信技能树 的这篇 Nature Genetics 杂志特别版单细胞 marker 基因气泡图，我也是在下面评论了一下后续有时间更新一下。这次对代码进行了更新，使用 ggplot 4.0.0 应该是没有问题的。

安装

install.packages(“devtools”)

devtools::install_github(“junjunlab/jjAnno”)
示例
画个基础图形：
library(jjAnno)
library(scales)
library(ggplot2)

data(“dot_data”)

add cell group

dot_data$cellGroup <- case_when(
dot_data$cell %in% c(“1b CoelEpi GATA4”, “2a Early somatic”, “2b ESGC male”) ~ “cell type1”,
dot_data$cell %in% c(“2b ESGC female”, “2c PreGC-I”, “2d Sertoil”) ~ “cell type2”,
dot_data$cell %in% c(“3a Early sPAX8”, “3b Gi”) ~ “cell type3”
)

order

dot_data$gene <- factor(dot_data$gene,levels = unique(dot_data$gene))

plot

pdot <-
ggplot(dot_data,aes(x = gene,y = cell)) +
geom_point(aes(fill = mean.expression,size = percentage),
color = ‘black’,
shape = 21) +
theme_bw(base_size = 14) +
xlab(”) + ylab(”) +
scale_fill_gradient2(low = ‘white’,mid = ‘#EB1D36’,high = ‘#990000’,
midpoint = 0.5,
name = ‘Mean expression’) +
scale_size(range = c(1,13)) +
theme(panel.grid = element_blank(),
axis.text = element_text(color = ‘black’),
aspect.ratio = 0.5,
plot.margin = margin(t = 1,r = 1,b = 1,l = 1,unit = ‘cm’),
axis.text.x = element_text(angle = 90,hjust = 1,vjust = 0.5,
face = ‘italic’)) +
coord_cartesian(clip = ‘off’)

pdot

添加注释：

add segment

annoSegment(object = pdot,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = 8.8,
segWidth = 0.5)

添加链接框：

add branch

annoSegment(object = pdot,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = 8.8,
segWidth = 0.5,
addBranch = T,
lwd = 2,
branDirection = -1,
pCol = rep(‘black’,11))

文字标签：

add text

annoSegment(object = pdot,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = 8.8,
segWidth = 0.5,
addText = T,
textRot = 45,
hjust = 0)

细胞分组：

mapping cell group

annoSegment(object = pdot,
annoPos = ‘left’,
aesGroup = T,
aesGroName = ‘cellGroup’,
xPosition = -3.5,
segWidth = 0.5,
addText = T,
textRot = 90,
textHVjust = -0.5,
textSize = 14)

添加矩形注释：

mapping by group

annoRect(object = pdot,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = c(9,9.5),
rectWidth = 0.8)

add to botomn

annoRect(object = pdot,
annoPos = ‘botomn’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = c(-2,0.25),
rectWidth = 0.8,
alpha = 0.35)

mapping cell group

annoRect(object = pdot,
annoPos = ‘left’,
aesGroup = T,
aesGroName = ‘cellGroup’,
xPosition = c(-3.5,0.25),
alpha = 0.3,
rectWidth = 0.8,
addText = T,
textRot = 90,
textSize = 14,
textCol = rep(‘black’,3),
textHVjust = -2.3)

添加倾斜矩形：

add group label

annoRect(object = pdot_test,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
yPosition = c(8.6,10.4),
rotateRect = T,
alpha = 0.5,
rectWidth = 0.9,
rectAngle = 50,
normRectShift = 0.15,
addText = T,
textHVjust = 1,
textRot = 60,
hjust = 0,
textShift = 0.5)

点注释：

add text label

annoPoint2(object = pdot,
annoPos = ‘top’,
aesGroup = T,
aesGroName = ‘class’,
ptSize = 2,
yPosition = 9,
addText = T,
textRot = 45,
hjust = 0,
textHVjust = 0.4)

还有一些其他好玩的，大家可以自己去看看说明文档。
结尾
路漫漫其修远兮,吾将上下而求索。
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