说明：hhh{bbb}中hhh指函数，bbb指包名。
01
—
ggdensity{ggpubr}
密度图
代码语言：javascript复制library(ggpubr)
## 创建数据
set.seed(1024)
dt = data.frame(
sex = factor(rep(c("F", "M"), each=200)),
weight = c(rnorm(200, 55), rnorm(200, 58)))
head(dt, 3)
# sex weight
# 1 F 54.22134
# 2 F 54.61052
# 3 F 52.96620
## 制图
ggdensity(dt, x = "weight",
add = "mean", rug = TRUE,
color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))
ggdensity
代码语言：javascript复制## 创建数据
set.seed(1024)
dt = data.frame(
sex = factor(rep(c("F", "M"), each=200)),
weight = c(rnorm(200, 55), rnorm(200, 58)))
## 制图
gghistogram(dt, x = "weight",
add = "mean", rug = TRUE,
color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))
02
—
ggboxplot{ggpubr}
Box plots
代码语言：javascript复制
library(ggpubr)
## 数据
data("ToothGrowth")
df <- ToothGrowth
head(df, 4)
# 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
# 图
p <- ggboxplot(df, x = "dose", y = "len",
color = "dose", palette =c("#00AFBB", "#E7B800", "#FC4E07"),
add = "jitter", shape = "dose")
p
library(ggpubr)
## 数据
data("ToothGrowth")
df <- ToothGrowth
head(df, 4)
# 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
## 图
p <- ggboxplot(df, x = "dose", y = "len",
color = "dose", palette =c("#00AFBB", "#E7B800", "#FC4E07"),
add = "jitter", shape = "dose")
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
p stat_compare_means(comparisons = my_comparisons)
stat_compare_means(label.y = 50)
03
—
ggbarplot{ggpubr}
bar plots
代码语言：javascript复制library(ggpubr)
# 数据
data("mtcars")
dfm <- mtcars
# Convert the cyl variable to a factor 转换数据类型
dfm$cyl <- as.factor(dfm$cyl)
# Add the name colums
dfm$name <- rownames(dfm)
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg",
fill = "cyl", # change fill color by cyl
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "desc", # Sort the value in dscending order
sort.by.groups = FALSE, # Don't sort inside each group
x.text.angle = 90 # Rotate vertically x axis texts
)
library(ggpubr)
# 数据
data("mtcars")
dfm <- mtcars
# Convert the cyl variable to a factor 转换数据类型
dfm$cyl <- as.factor(dfm$cyl)
# Add the name colums
dfm$name <- rownames(dfm)
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg",
fill = "cyl", # change fill color by cyl
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "asc", # Sort the value in dscending order
sort.by.groups = TRUE, # Sort inside each group
x.text.angle = 90 # Rotate vertically x axis texts
)
library(ggpubr)
# Calculate the z-score of the mpg data
dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
levels = c("low", "high"))
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "mpg_z", "mpg_grp", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg_z",
fill = "mpg_grp", # change fill color by mpg_level
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "asc", # Sort the value in ascending order
sort.by.groups = FALSE, # Don't sort inside each group
x.text.angle = 90, # Rotate vertically x axis texts
ylab = "MPG z-score",
xlab = FALSE,
legend.title = "MPG Group"
)
library(ggpubr)
# Calculate the z-score of the mpg data
dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
levels = c("low", "high"))
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "mpg_z", "mpg_grp", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg_z",
fill = "mpg_grp", # change fill color by mpg_level
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "desc", # Sort the value in descending order
sort.by.groups = FALSE, # Don't sort inside each group
x.text.angle = 90, # Rotate vertically x axis texts
ylab = "MPG z-score",
legend.title = "MPG Group",
rotate = TRUE,
ggtheme = theme_minimal()
)04
—
ggdotchart{ggpubr}
Dot chart
代码语言：javascript复制library(ggpubr)
# Calculate the z-score of the mpg data
dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
levels = c("low", "high"))
ggdotchart(dfm, x = "name", y = "mpg",
color = "cyl", # Color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
sorting = "ascending", # Sort value in descending order
add = "segments", # Add segments from y = 0 to dots
ggtheme = theme_pubr() # ggplot2 theme
)
library(ggpubr)
# Calculate the z-score of the mpg data
dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
levels = c("low", "high"))
ggdotchart(dfm, x = "name", y = "mpg",
color = "cyl", # Color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
sorting = "descending", # Sort value in descending order
add = "segments", # Add segments from y = 0 to dots
rotate = TRUE, # Rotate vertically
group = "cyl", # Order by groups
dot.size = 6, # Large dot size
label = round(dfm$mpg), # Add mpg values as dot labels
font.label = list(color = "white", size = 9,
vjust = 0.5), # Adjust label parameters
ggtheme = theme_pubr() # ggplot2 theme
)
library(ggpubr)
# Calculate the z-score of the mpg data
dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
levels = c("low", "high"))
ggdotchart(dfm, x = "name", y = "mpg_z",
color = "cyl", # Color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
sorting = "descending", # Sort value in descending order
add = "segments", # Add segments from y = 0 to dots
add.params = list(color = "lightgray", size = 2), # Change segment color and size
group = "cyl", # Order by groups
dot.size = 6, # Large dot size
label = round(dfm$mpg_z,1), # Add mpg values as dot labels
font.label = list(color = "white", size = 9,
vjust = 0.5), # Adjust label parameters
ggtheme = theme_pubr() # ggplot2 theme
)
geom_hline(yintercept = 0, linetype = 2, color = "lightgray")
ggdotchart(dfm, x = "name", y = "mpg",
color = "cyl", # Color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
sorting = "descending", # Sort value in descending order
rotate = TRUE, # Rotate vertically
dot.size = 2, # Large dot size
y.text.col = TRUE, # Color y text by groups
ggtheme = theme_pubr() # ggplot2 theme
)
theme_cleveland()
参考来源http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/
