R包ggpubr绘制发表级别图片

作者: Seurat_Satija | 来源:发表于2021-09-22 22:57 被阅读0次

R包ggpubr绘制发表级别图片
ggpubr——绘制各种SCI发表级箱图
R语言|lollipop plot
ggpubr绘图(1)
R-4.0.5 环境下安装R包ggpubr时，car无法安装，q
ggpubr包系列学习教程(二)
ggpubr包学习（一）
绘制有相关性信息和边际直方图的完美散点图
R语言可视化（三十一）：棒棒糖图绘制
R语言可视化（六）：饼图绘制

Hadley Wickham创建的可视化包ggplot2可以流畅地进行优美的可视化，但是如果要通过ggplot2定制一套图形，尤其是适用于杂志期刊等出版物的图形，对于那些没有深入了解ggplot2的人来说就有点困难了，ggplot2的部分语法是很晦涩的。为此Alboukadel Kassambara创建了基于ggplot2的可视化包ggpubr用于绘制符合出版物要求的图形。

安装及加载ggpubr包

安装方式有两种：

直接从CRAN安装：

install.packages("ggpubr")

从GitHub上安装最新版本：

if(!require(devtools)) install.packages("devtools")
 devtools::install_github("kassambara/ggpubr")

安装完之后直接加载就行：

library(ggpubr)

ggpubr可绘制图形：

ggpubr可绘制大部分我们常用的图形，下面一一介绍。

分布图(Distribution)

#构建数据集
set.seed(1234)
df <- data.frame( sex=factor(rep(c("f", "M"), each=200)), 
weight=c(rnorm(200, 55), rnorm(200, 58)))
head(df)

##   sex   weight
## 1  f   53.79293
## 2  f   55.27743
## 3  f   56.08444
## 4  f   52.65430
## 5  f   55.42912
## 6  f   55.50606

密度分布图以及边际地毯线并添加平均值线

ggdensity(df, x="weight", add = "mean", rug = TRUE, color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))

image

带有均值线和边际地毯线的直方图

gghistogram(df, x="weight", add = "mean", rug = TRUE, color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))

image

箱线图与小提琴图

#加载数据集ToothGrowth
data("ToothGrowth")
df1 <- ToothGrowth
head(df1)

##    len  supp  dose
## 1  4.2   VC    0.5
## 2  11.5  VC    0.5
## 3  7.3   VC    0.5
## 4  5.8   VC    0.5
## 5  6.4   VC    0.5
## 6  10.0  VC    0.5

p <- ggboxplot(df1, x="dose", y="len", color = "dose", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), 
add = "jitter", shape="dose")#增加了jitter点，点shape由dose映射p

image

增加不同组间的p-value值，可以自定义需要标注的组间比较

my_comparisons <- list(c("0.5", "1"), c("1", "2"), c("0.5", "2"))
p+stat_compare_means(comparisons = my_comparisons)+#不同组间的比较
stat_compare_means(label.y = 50)

image

内有箱线图的小提琴图

ggviolin(df1, x="dose", y="len", fill = "dose", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), 
add = "boxplot", add.params = list(fill="white"))+ 
stat_compare_means(comparisons = my_comparisons, label = "p.signif")+#label这里表示选择显著性标记（星号） 
stat_compare_means(label.y = 50)

image

条形图

data("mtcars")
df2 <- mtcars
df2$cyl <- factor(df2$cyl)
df2$name <- rownames(df2)#添加一行name
head(df2[, c("name", "wt", "mpg", "cyl")])

image

按从小到大顺序绘制条形图（不分组排序）

ggbarplot(df2, x="name", y="mpg", fill = "cyl", color = "white", 
palette = "jco",#杂志jco的配色 
sort.val = "desc",#下降排序 
sort.by.groups=FALSE,#不按组排序 
x.text.angle=60)

image

按组进行排序

ggbarplot(df2, x="name", y="mpg", fill = "cyl", color = "white", 
palette = "jco",#杂志jco的配色 
sort.val = "asc",#上升排序,区别于desc，具体看图演示 
sort.by.groups=TRUE,#按组排序 
x.text.angle=90)

image

偏差图

偏差图展示了与参考值之间的偏差

df2$mpg_z <- (df2$mpg-mean(df2$mpg))/sd(df2$mpg)
df2$mpg_grp <- factor(ifelse(df2$mpg_z<0, "low", "high"), levels = c("low", "high"))
head(df2[, c("name", "wt", "mpg", "mpg_grp", "cyl")])

image

绘制排序过的条形图

ggbarplot(df2, x="name", y="mpg_z", fill = "mpg_grp", color = "white", 
palette = "jco", sort.val = "asc", sort.by.groups = FALSE, x.text.angle=60, 
ylab = "MPG z-score", xlab = FALSE, legend.title="MPG Group")

image

坐标轴变换

ggbarplot(df2, x="name", y="mpg_z", fill = "mpg_grp", color = "white", 
palette = "jco", sort.val = "desc", sort.by.groups = FALSE, 
x.text.angle=90, ylab = "MPG z-score", xlab = FALSE, 
legend.title="MPG Group", rotate=TRUE, ggtheme = theme_minimal())

image

点图(Dot charts)

棒棒糖图(Lollipop chart)

棒棒图可以代替条形图展示数据

ggdotchart(df2, x="name", y="mpg", color = "cyl", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), sorting = "ascending", 
add = "segments", ggtheme = theme_pubr())

image

可以自设置各种参数

ggdotchart(df2, x="name", y="mpg", color = "cyl", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), sorting = "descending", 
add = "segments", rotate = TRUE, group = "cyl", dot.size = 6, 
label = round(df2$mpg), font.label = list(color="white", size=9, vjust=0.5), 
ggtheme = theme_pubr())

image

偏差图

ggdotchart(df2, x="name", y="mpg_z", color = "cyl", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), sorting = "descending", 
add = "segment", add.params = list(color="lightgray", size=2), 
group = "cyl", dot.size = 6, label = round(df2$mpg_z, 1), 
font.label = list(color="white", size=9, vjust=0.5), ggtheme = theme_pubr())+ 
geom_line(yintercept=0, linetype=2, color="lightgray")

image

Cleveland点图

ggdotchart(df2, x="name", y="mpg", color = "cyl", 
palette = c("#00AFBB", "#E7B800", "#FC4E07"), sorting = "descending", 
rotate = TRUE, dot.size = 2, y.text.col=TRUE, ggtheme = theme_pubr())+ 
theme_cleveland()