其他
jjAnno 优雅的帮你添加注释
人从众𠈌
1引言
冰冻三尺,非一日之寒,见的图多了,于是渐渐发现自己的绘图会遇到一些瓶颈。下次再遇见则艰难的踌躇不前。
绘图的时候,大部分我们都是在图里进行各种操作的,但是在图外(坐标轴外)画图好像不是一件容易的事,当然是有解决方案的,比如 Ai 或者 Ps, 又或者多写一些代码来完成,我们看看下面这张来自 nature 文章的部分图片:
你会不会好奇图旁边那些各种各样的注释 (文字,线段,矩形等等)是如何添加的?有没有 R 包可以做这样的事情?
好在 ggplot 提供了一个 annotation_custom 这样一个函数可以基于 grid 基础上绘制一些基础图形, 于是我对一些基础函数进行了封装,编写了 jjAnno 这样一个包,可以方便的在图像上添加不同类型的注释。
可以做什么:
useMyCol: 提供 ArchR 包里的颜色。 annoPoint: 添加点注释。 annoRect: 添加矩形注释。 annoSegment: 添加线段注释。 annoImage: 添加图片注释。 annoLegend: 添加图例注释。
2安装
# install.packages("devtools")
devtools::install_github("junjunlab/jjAnno")
library(jjAnno)
github 地址:
https://github.com/junjunlab/jjAnno
参考手册地址:
https://github.com/junjunlab/jjAnno/wiki/jjAnno-0.0.1
注意:
你的 ggplot 图应该加上:
coord_cartesian(clip = 'off')
3useMyCol
查看所有颜色主题名称:
# show all plattes
useMyCol(showAll = T)
# [1] "stallion" "stallion2" "calm" "kelly" "bear" "ironMan"
# [7] "circus" "paired" "grove" "summerNight" "zissou" "darjeeling"
# [13] "rushmore" "captain" "horizon" "horizonExtra" "blueYellow" "sambaNight"
# [19] "solarExtra" "whitePurple" "whiteBlue" "comet" "greenBlue" "beach"
# [25] "coolwarm" "fireworks" "greyMagma" "fireworks2" "purpleOrange"
绘制颜色:
# plot colors
show_col(useMyCol('stallion',20))
# ironMan
show_col(useMyCol('ironMan',15))
# whitePurple
show_col(useMyCol('whitePurple',9))
4annoPoint
annoPoint 用来给图形添加点注释。
加载测试数据
测试数据:
df <- data.frame(x = 1:10,y = sample(1:10,10),
x1 = LETTERS[1:10])
绘图:
library (ggplot2)
p <-
ggplot(df, aes(x,x1)) +
geom_point(aes(size = x,color = x,alpha = x)) +
theme_bw(base_size = 14) +
scale_x_continuous(breaks = seq(1,10,1)) +
# scale_y_continuous(breaks = seq(1,10,1)) +
scale_color_gradient(low = 'grey50',high = '#339933',name = '') +
coord_cartesian(clip = 'off') +
theme(aspect.ratio = 1,
plot.margin = margin(t = 1,r = 1,b = 1,l = 1,unit = 'cm'),
axis.text.x = element_text(vjust = unit(-1.5,'native')),
legend.position = 'left') +
xlab('') + ylab('')
p
或者使用包里的内置数据:
data(p)
添加注释
简单绘图:
# default plot
annoPoint(object = p,
annoPos = 'top',
xPosition = c(1:10))
指定多个 yPosition:
# specify yPosition
annoPoint(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = rep(c(2,4,2,6,4),each = 2))
添加到右边:
# add right
annoPoint(object = p,
annoPos = 'right',
yPosition = c(1:10))
添加到左边:
# left
annoPoint(object = p,
annoPos = 'left',
yPosition = c(1:10))
调整 xPosition:
# supply xPosition to ajust
annoPoint(object = p,
annoPos = 'right',
yPosition = c(1:10),
xPosition = 0.3)
改变点大小和形状:
# change point size and shape
annoPoint(object = p,
annoPos = 'top',
xPosition = c(1:10),
ptSize = 2,
ptShape = 25)
添加多层注释::
# add multiple annotations
p1 <- annoPoint(object = p,
annoPos = 'top',
xPosition = c(1:10),
ptSize = 2,
ptShape = 25)
annoPoint(object = p1,
annoPos = 'right',
yPosition = c(1:10),
ptSize = 2,
ptShape = 23)
5annoRect
annoRect 用来给图添加矩形注释。
简单绘图:
# default plot
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10))
调整 yPosition:
# adjust yPosition
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5))
调整透明度:
# change color alpha
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5),
alpha = 0.5)
设置矩形宽度:
# adjust rectWidth
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5),
rectWidth = 0.9)
改变边缘颜色和填充颜色:
# change rect color and fill
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5),
rectWidth = 0.9,
pCol = rep('black',10),
pFill = rep('grey80',10))
调整矩形线型和线粗:
# change rect lty and lwd
annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5),
rectWidth = 0.9,
pCol = rep('black',10),
pFill = rep('grey80',10),
lty = 'dashed',
lwd = 2)
添加部分注释:
# only add some annotations
annoRect(object = p,
annoPos = 'top',
xPosition = c(1,3,5,7,9),
yPosition = c(11,11.5))
手动添加注释:
# supply your own coordinates to annotate
annoRect(object = p,
annoPos = 'top',
annoManual = T,
xPosition = list(c(1,6),
c(5,10)),
yPosition = c(11,11.5),
pCol = rep('black',2),
lty = 'solid',
lwd = 2)
多个不同矩形的 yPosition:
# multiple yPosition
annoRect(object = p,
annoPos = 'top',
annoManual = T,
xPosition = list(c(1,6),
c(5,10)),
yPosition = list(c(11,11.5),
c(11.5,12)),
pCol = rep('black',2),
lty = 'solid',
lwd = 2)
添加到右边:
# add to right
annoRect(object = p,
annoPos = 'right',
yPosition = c(1:10),
xPosition = c(10.5,11),
rectWidth = 0.8)
添加多个注释:
# add multiple
p1 <- annoRect(object = p,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11,11.5),
rectWidth = 0.9,
pCol = rep('black',10),
pFill = rep('grey80',10),
lty = 'dashed',
lwd = 2)
# add second annotation
p2 <- annoRect(object = p1,
annoPos = 'right',
yPosition = c(1:10),
xPosition = c(10.5,11),
rectWidth = 0.8)
# add third annotation
annoRect(object = p2,
annoPos = 'top',
xPosition = c(1:10),
yPosition = c(11.8,12.3),
rectWidth = 0.8)
add GO plot with annotation
加载测试数据:
data(pgo)
pgo
绘图:
# Plot
pgo <-
ggplot(df1,aes(x = log10PValue,y = Term)) +
geom_point(aes(size = log10PValue,
color = log10PValue)) +
scale_color_gradient2(low = 'blue',mid = 'green',high = 'red',
name = '',midpoint = 2.1) +
scale_y_discrete(position = 'right') +
scale_x_continuous(breaks = seq(0,2.8,0.4),limits = c(0,2.8)) +
theme_grey(base_size = 14) +
theme(legend.position = 'left',
plot.margin = margin(t = 1,r = 1,b = 1,l = 1,unit = 'cm'),
aspect.ratio = 2.5
) +
coord_cartesian(clip = 'off') +
ylab('')
annotate
添加 15 个矩形:
# another example annotation GO terms
annoRect(object = pgo,
annoPos = 'right',
yPosition = c(1:15),
pCol = rep('transparent',15),
pFill = rep(c('#F5F0BB','#C4DFAA','#90C8AC'),each = 5),
xPosition = c(3,10),
rectWidth = 1)
手动添加 3 个矩形注释:
# annotate mannually
annoRect(object = pgo,
annoPos = 'right',
annoManual = T,
xPosition = c(3,10),
yPosition = list(c(0.5,5.5,10.5),
c(5.5,10.5,15.5)),
pCol = rep('black',3),
pFill = c('#F5F0BB','#C4DFAA','#90C8AC'))
6annoSegment
annoSegment 用来给图添加线段。
简单绘图:
# default plot
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10))
调整矩形宽度:
# adjust rectWidth
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8)
添加箭头:
library(ggplot2)
# add segments with arrow
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.9,
lwd = 1,
mArrow = arrow(ends = 'both',
length = unit(0.2,'cm'),
type = 'closed'))
设置颜色:
# change rect color and fill
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
pCol = useMyCol('horizon',10))
添加分支:
# add branch
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4)
调整分支方向:
# change branch direction
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4,
branDirection = -1)
添加到底部:
# add to botomn
annoSegment(object = p,
annoPos = 'botomn',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4)
添加到右边:
# add to right
annoSegment(object = p,
annoPos = 'right',
yPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4,
branDirection = -1)
给分支添加箭头:
# add to botomn and make branch taged with arrow
annoSegment(object = p,
annoPos = 'botomn',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 3,
bArrow = arrow(length = unit(0.2,'cm'),
ends = 'last'))
添加文字:
# add text label
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4,
branDirection = -1,
addText = T,
textLabel = paste0('anno',1:10,sep = ''),
textRot = 0,
textSize = 15)
调整文字:
# add text space from segments
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4,
branDirection = -1,
addText = T,
textLabel = paste0('anno',1:10,sep = ''),
textRot = 45,
textSize = 15,
textHVjust = 0.5)
改变颜色:
# change text color
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
addBranch = T,
lwd = 4,
branDirection = -1,
addText = T,
textLabel = paste0('anno',1:10,sep = ''),
textRot = 45,
textSize = 15,
textHVjust = 0.5,
textCol = rep('grey50',10))
调整 yPosition:
# change yPosition
annoSegment(object = p,
annoPos = 'top',
xPosition = c(1:10),
segWidth = 0.8,
pCol = useMyCol('horizon',10),
yPosition = 5)
手动注释:
# supply your own coordinates to annotate
annoSegment(object = p,
annoPos = 'top',
annoManual = T,
xPosition = list(c(1,6),
c(5,10)),
yPosition = 11,
pCol = c('green','orange'))
添加分支:
# add branch to plot
annoSegment(object = p,
annoPos = 'top',
annoManual = T,
addBranch = T,
lwd = 3,
segWidth = 0.5,
xPosition = list(c(1,6),
c(5,10)),
yPosition = c(11,11),
pCol = c('green','orange'),
branDirection = -1)
添加到右边:
# add to right
annoSegment(object = p,
annoPos = 'right',
yPosition = c(1:10),
segWidth = 0.8)
注释 GO 图形:
# annotate mannually
annoSegment(object = pgo,
annoPos = 'left',
annoManual = T,
xPosition = rep(-0.15,3),
yPosition = list(c(1,6,11),
c(5,10,15)),
pCol = c('#F5F0BB','#C4DFAA','#90C8AC'),
segWidth = 1)
7annoImage
annoImage 用来给图添加图形注释。
加载内置图形:
img1 <- system.file("extdata/animal-img/", "1.jpg", package = "jjAnno")
img2 <- system.file("extdata/animal-img/", "2.jpg", package = "jjAnno")
img3 <- system.file("extdata/animal-img/", "3.jpg", package = "jjAnno")
img4 <- system.file("extdata/animal-img/", "4.jpg", package = "jjAnno")
img5 <- system.file("extdata/animal-img/", "5.jpg", package = "jjAnno")
img6 <- system.file("extdata/animal-img/", "6.jpg", package = "jjAnno")
img7 <- system.file("extdata/animal-img/", "7.jpg", package = "jjAnno")
img8 <- system.file("extdata/animal-img/", "8.jpg", package = "jjAnno")
img9 <- system.file("extdata/animal-img/", "9.jpg", package = "jjAnno")
img10 <- system.file("extdata/animal-img/", "10.jpg", package = "jjAnno")
imgs <- c(img1,img2,img3,img4,img5,img6,img7,img8,img9,img10)
简单绘制:
# add legend
annoImage(object = p,
annoPos = 'top',
xPosition = c(1:10),
images = imgs,
yPosition = c(11,12))
调整宽度:
# change width
annoImage(object = p,
annoPos = 'top',
xPosition = c(1:10),
images = imgs,
yPosition = c(11,11.8),
segWidth = 0.8)
Add to right:
# add to right
annoImage(object = p,
annoPos = 'right',
yPosition = c(1:10),
images = imgs,
xPosition = c(11,11.8),
segWidth = 0.8)
添加到底部:
# add to botomn
annoImage(object = p,
annoPos = 'botomn',
xPosition = c(1:10),
images = imgs,
yPosition = c(-1.2,-0.4),
segWidth = 0.8)
手动注释:
# annotate manually
annoImage(object = p,
annoPos = 'right',
yPosition = list(c(1:10),
c(1:10)),
images = imgs,
annoManual = T,
xPosition = list(rep(c(11,11.8),each = 5),
rep(c(11.8,12.6),each = 5)),
segWidth = 0.8)
8annoLegend
annoLegend 用来给图添加图例注释。
简单注释:
# add legend
annoLegend(object = p,
labels = paste('legend ',1:5),
pch = 21,
col = 'black',
fill = useMyCol('paired',5),
textSize = 15)
调整位置:
# change pos
annoLegend(object = p,
relPos = c(0.2,0.9),
labels = paste('legend ',1:5),
pch = 21,
col = 'black',
fill = useMyCol('paired',5),
textSize = 15)
设置不同形状:
# multiple shapes
annoLegend(object = p,
relPos = c(0.2,0.9),
labels = paste('legend ',1:5),
pch = 21:25,
col = 'black',
fill = useMyCol('paired',5),
textSize = 15)
自定义坐标:
# define x and y position
annoLegend(object = p,
xPosition = 12,
yPosition = 5,
labels = paste('legend ',1:5),
pch = 21:25,
col = 'black',
fill = useMyCol('paired',5),
textSize = 15)
9示例
加载内置数据:
data("pdot")
pdot
添加注释:
# add segment
P1 <- annoSegment(object = pdot,
annoPos = 'top',
xPosition = c(1:21),
yPosition = 8.8,
segWidth = 0.7,
pCol = c(useMyCol('stallion',20),'orange'))
# add rect1
P2 <- annoRect(object = P1,
annoPos = 'left',
annoManual = T,
yPosition = list(c(0.5,4.5),
c(4.5,8.5)),
xPosition = c(-3.5,0.3),
pCol = rep('white',2),
pFill = useMyCol('calm',2),
alpha = 0.5)
# add rect2
P3 <- annoRect(object = P2,
annoPos = 'left',
annoManual = T,
yPosition = list(c(2.5),
c(6.5)),
xPosition = c(-3.5,16.5),
pCol = 'black',
pFill = 'transparent',
lty = 'dashed',
lwd = 3)
# add branch
P4 <- annoSegment(object = P3,
annoPos = 'top',
annoManual = T,
xPosition = list(c(1,3,4,7,9,11,12,15,17,19,20),
c(2,3,6,8,10,11,14,16,18,19,21)),
yPosition = 9.2,
segWidth = 0.8,
pCol = rep('black',11),
addBranch = T,
branDirection = -1,
lwd = 3)
# add text
text <- c('Mesothelial','Extragonadal','Gonadal','Supporting lineage','Interstitial lineage',
'Testis fate','Early supporting','Granulosa','Sertoli','sPAX8','Mesenchymal')
# add segment branch and text
annoSegment(object = P4,
annoPos = 'top',
annoManual = T,
xPosition = list(c(1,3,4,7,9,11,12,15,17,19,20),
c(2,3,6,8,10,11,14,16,18,19,21)),
yPosition = 9.2,
segWidth = 0.8,
pCol = rep('black',11),
addBranch = T,
branDirection = -1,
lwd = 3,
addText = T,
textLabel = text,
textCol = c(rep('black',5),'blue',rep('black',5)),
textRot = 45,
hjust = 0)
10结尾
更多参数见:
?useMyCol
?annoPoint
?annoRect
?annoSegment
?annoImage
?annoLegend
有其它建议或者疑问请在 github 提问。
欢迎加入生信交流群。加我微信我也拉你进 微信群聊 老俊俊生信交流群 (微信交流群需收取20元入群费用(防止骗子和便于管理))。
老俊俊微信：
知识星球：
所以今天你学习了吗？
今天的分享就到这里了，敬请期待下一篇！
最后欢迎大家分享转发，您的点赞是对我的鼓励和肯定！
如果觉得对您帮助很大，赏杯快乐水喝喝吧！
往期回顾
◀...