R語言可視化學習筆記之ggpubr包

01-27

作者簡介Introduction

taoyan：偽碼農，R語言愛好者，愛開源。

個人博客: https://ytlogos.github.io/

往期回顧

R語言學習筆記之聚類分析

Hadley Wickham創建的可視化包ggplot2可以流暢地進行優美的可視化，但是如果要通過ggplot2定製一套圖形，尤其是適用於雜誌期刊等出版物的圖形，對於那些沒有深入了解ggplot2的人來說就有點困難了，ggplot2的部分語法是很晦澀的。為此Alboukadel Kassambara創建了基於ggplot2的可視化包ggpubr用於繪製符合出版物要求的圖形。

安裝及載入ggpubr包

安裝方式有兩種：

直接從CRAN安裝：

install.packages("ggpubr")

從GitHub上安裝最新版本：

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

安裝完之後直接載入就行：

library(ggpubr)

ggpubr可繪製圖形

ggpubr可繪製大部分我們常用的圖形，下面一一介紹。

分布圖(Distribution)

#構建數據集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

密度分布圖以及邊際地毯線並添加平均值線

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

帶有均值線和邊際地毯線的直方圖

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

箱線圖與小提琴圖

#載入數據集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點，點shape由dose映射p

增加不同組間的p-value值，可以自定義需要標註的組間比較

my_comparisons <- list(c("0.5", "1"), c("1", "2"), c("0.5", "2")) p+stat_compare_means(comparisons = my_comparisons)+#不同組間的比較stat_compare_means(label.y=50)

內有箱線圖的小提琴圖

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這裡表示選擇顯著性標記（星號）
stat_compare_means(label.y = 50)

條形圖

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")])

按從小到大順序繪製條形圖（不分組排序）

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

按組進行排序

ggbarplot(df2, x="name", y="mpg", fill = "cyl", color = "white",
palette = "jco",#雜誌jco的配色
sort.val = "asc",#上升排序,區別於desc，具體看圖演示

sort.by.groups=TRUE,#按組排序
x.text.angle=90)

偏差圖

偏差圖展示了與參考值之間的偏差

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")])

繪製排序過的條形圖

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")

坐標軸變換

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())

點圖(Dot charts)

棒棒糖圖(Lollipop chart)

棒棒圖可以代替條形圖展示數據

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

add = "segments", ggtheme = theme_pubr())

可以自設置各種參數

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())

偏差圖

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")

Cleveland點圖

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()

SessionInfo

sessionInfo()

## R version 3.4.0 (2017-04-21)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 8.1 x64 (build 9600)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936
## [2] LC_CTYPE=Chinese (Simplified)_China.936
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C
## [5] LC_TIME=Chinese (Simplified)_China.936
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggpubr_0.1.3 magrittr_1.5 ggplot2_2.2.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.11 knitr_1.16 munsell_0.4.3 colorspace_1.3-2
## [5] R6_2.2.1 rlang_0.1.1 stringr_1.2.0 plyr_1.8.4
## [9] dplyr_0.5.0 tools_3.4.0 grid_3.4.0 gtable_0.2.0
## [13] DBI_0.6-1 htmltools_0.3.6 yaml_2.1.14 lazyeval_0.2.0
## [17] rprojroot_1.2 digest_0.6.12 assertthat_0.2.0 tibble_1.3.3
## [21] ggsignif_0.2.0 ggsci_2.4 purrr_0.2.2.2 evaluate_0.10
## [25] rmarkdown_1.5 labeling_0.3 stringi_1.1.5 compiler_3.4.0
## [29] scales_0.4.1 backports_1.1.0

往期精彩內容整理合集

2017年R語言發展報告（國內）

R語言中文社區歷史文章整理（作者篇）

R語言中文社區歷史文章整理（類型篇）