如果觉得ggplot2对你来说还是太难， 可以尝试用ggpur ...
ggplot2, by Hadley Wickham, is an excellent and flexible package for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a ggplot, the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills.
The ‘ggpubr’ package provides some easy-to-use functions for creating and customizing ‘ggplot2’- based publication ready plots.
Find out more at https://rpkgs.datanovia.com/ggpubr.
安装与加载ggpur
- Install from CRAN as follow:
install.packages("ggpubr")
- Or, install the latest version from GitHub as follow:
# Install
if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")
1. 频数分布图
library(ggpubr)
#> Le chargement a nécessité le package : ggplot2
#> Le chargement a nécessité le package : magrittr
# Create some data format
# :::::::::::::::::::::::::::::::::::::::::::::::::::
set.seed(1234)
wdata = data.frame(
sex = factor(rep(c("F", "M"), each=200)),
weight = c(rnorm(200, 55), rnorm(200, 58)))
head(wdata, 4)
#> sex weight
#> 1 F 53.79293
#> 2 F 55.27743
#> 3 F 56.08444
#> 4 F 52.65430
# Density plot with mean lines and marginal rug
# :::::::::::::::::::::::::::::::::::::::::::::::::::
# Change outline and fill colors by groups ("sex")
# Use custom palette
ggdensity(wdata, x = "weight",
add = "mean", rug = TRUE,
color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))
图片.png
# Histogram plot with mean lines and marginal rug
# :::::::::::::::::::::::::::::::::::::::::::::::::::
# Change outline and fill colors by groups ("sex")
# Use custom color palette
gghistogram(wdata, x = "weight",
add = "mean", rug = TRUE,
color = "sex", fill = "sex",
palette = c("#00AFBB", "#E7B800"))
图片.png
2. 箱线图和小提琴图
# Load data
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
# Box plots with jittered points
# :::::::::::::::::::::::::::::::::::::::::::::::::::
# Change outline colors by groups: dose
# Use custom color palette
# Add jitter points and change the shape by groups
p <- ggboxplot(df, x = "dose", y = "len",
color = "dose", palette =c("#00AFBB", "#E7B800", "#FC4E07"),
add = "jitter", shape = "dose")
p
图片.png
# Add p-values comparing groups
# Specify the comparisons you want
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
p + stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
stat_compare_means(label.y = 50) # Add global p-value
图片.png
# Violin plots with box plots inside
# :::::::::::::::::::::::::::::::::::::::::::::::::::
# Change fill color by groups: dose
# add boxplot with white fill color
ggviolin(df, 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")+ # Add significance levels
stat_compare_means(label.y = 50) # Add global the p-value
图片.png
3. 柱状图
Demo data set
Load and prepare data:
# Load data
data("mtcars")
dfm <- mtcars
# Convert the cyl variable to a factor
dfm$cyl <- as.factor(dfm$cyl)
# Add the name colums
dfm$name <- rownames(dfm)
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "cyl")])
#> name wt mpg cyl
#> Mazda RX4 Mazda RX4 2.620 21.0 6
#> Mazda RX4 Wag Mazda RX4 Wag 2.875 21.0 6
#> Datsun 710 Datsun 710 2.320 22.8 4
#> Hornet 4 Drive Hornet 4 Drive 3.215 21.4 6
#> Hornet Sportabout Hornet Sportabout 3.440 18.7 8
#> Valiant Valiant 3.460 18.1 6
3.1. 有序柱状图
Change the fill color by the grouping variable “cyl”. Sorting will be done globally, but not by groups.
ggbarplot(dfm, x = "name", y = "mpg",
fill = "cyl", # change fill color by cyl
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "desc", # Sort the value in dscending order
sort.by.groups = FALSE, # Don't sort inside each group
x.text.angle = 90 # Rotate vertically x axis texts
)
图片.png
Sort bars inside each group. Use the argument sort.by.groups = TRUE.
ggbarplot(dfm, x = "name", y = "mpg",
fill = "cyl", # change fill color by cyl
color = "white", # Set bar border colors to white
palette = "jco", # jco journal color palett. see ?ggpar
sort.val = "asc", # Sort the value in dscending order
sort.by.groups = TRUE, # Sort inside each group
x.text.angle = 90 # Rotate vertically x axis texts
)
[图片上传失败...(image-13a3a9-1571188580112)]
3.2. 偏差图
The deviation graph shows the deviation of quantitatives values to a reference value. In the R code below, we’ll plot the mpg z-score from the mtcars dataset.
Calculate the z-score of the mpg data:
# Calculate the z-score of the mpg data
dfm$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")])
#> name wt mpg mpg_z mpg_grp cyl
#> Mazda RX4 Mazda RX4 2.620 21.0 0.1508848 high 6
#> Mazda RX4 Wag Mazda RX4 Wag 2.875 21.0 0.1508848 high 6
#> Datsun 710 Datsun 710 2.320 22.8 0.4495434 high 4
#> Hornet 4 Drive Hornet 4 Drive 3.215 21.4 0.2172534 high 6
#> Hornet Sportabout Hornet Sportabout 3.440 18.7 -0.2307345 low 8
#> Valiant Valiant 3.460 18.1 -0.3302874 low 6
Create an ordered barplot, colored according to the level of mpg:
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"
)
图片.png
3.3 旋转图形
ggtheme参数设置主题:
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()
)
图片.png
4.点图
4.1. Lollipop chart-棒棒糖图
Lollipop chart is an alternative to bar plots, when you have a large set of values to visualize.
Lollipop chart colored by the grouping variable “cyl”:
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
)
图片.png
- Sort in decending order. sorting = “descending”.
- Rotate the plot vertically, using rotate = TRUE.
- Sort the mpg value inside each group by using group = “cyl”.
- Set dot.size to 6.
- Add mpg values as label. label = “mpg” or label = round(dfm$mpg).
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$mpg), # Add mpg values as dot labels
font.label = list(color = "white", size = 9,
vjust = 0.5), # Adjust label parameters
ggtheme = theme_pubr() # ggplot2 theme
)
图片.png
4.2. Deviation graph:
- Use y = “mpg_z”
- Change segment color and size: add.params = list(color = “lightgray”, size = 2)
ggdotchart(dfm, x = "name", y = "mpg_z",
color = "cyl", # Color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
sorting = "descending", # Sort value in descending order
add = "segments", # Add segments from y = 0 to dots
add.params = list(color = "lightgray", size = 2), # Change segment color and size
group = "cyl", # Order by groups
dot.size = 6, # Large dot size
label = round(dfm$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")
图片.png
4.3. Cleveland’s dot plot
Color y text by groups. Use y.text.col = TRUE.
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() # Add dashed grids
图片.png
更多应用实例
密度图、频数图上加文字
By kassambara, The 02/09/2017 in ggpubr: Publication Ready Plots
Add Text Labels to Histogram and Density Plots
In this article, we’ll explain how to create histograms/density plots with text labels using the ggpubr package. I used this type of plots in my recent scientific publication entitled “Global... [Read more]
多图-组图、分面 ggplots: Easy Guide to Facet
By kassambara, The 02/09/2017 in ggpubr: Publication Ready Plots
Create and Customize Multi-panel ggplots: Easy Guide to Facet
This article describes how to split up your data by one or more variables and to visualize the subsets of the data together. The function facet() [in ggpubr] allows to draw multi-panel plots... [Read more]
ggplot2 - 修改图形参数
By kassambara, The 01/09/2017 in ggpubr: Publication Ready Plots
ggplot2 - Easy Way to Change Graphical Parameters
This article describes the function ggpar() [in ggpubr], which can be used to simply and easily customize any ggplot2-based graphs. The graphical parameters that can be changed using ggpar()... [Read more]
ggplot2 - 多图组图
By kassambara, The 01/09/2017 in ggpubr: Publication Ready Plots
ggplot2 - Easy Way to Mix Multiple Graphs on The Same Page
To arrange multiple ggplot2 graphs on the same page, the standard R functions - par() and layout() - cannot be used. The basic solution is to use the gridExtra R package, which comes with the... [Read more]
条形图+ Modern Alternatives
By kassambara, The 01/09/2017 in ggpubr: Publication Ready Plots
Bar Plots and Modern Alternatives
This article describes how to create easily basic and ordered bar plots using ggplot2 based helper functions available in the ggpubr R package. We’ll also present some modern alternatives to bar... [Read more]
均值、标准偏差做图
By kassambara, The 01/09/2017 in ggpubr: Publication Ready Plots
Plot Means/Medians and Error Bars
In this article, we’ll describe how to plot easily means or medians with error bars. We’ll use ggplot2 based helper functions available in the ggpubr R... [Read more]
散点图相关性分析+密度图
By kassambara, The 01/09/2017 in ggpubr: Publication Ready Plots
Perfect Scatter Plots with Correlation and Marginal Histograms
Scatter plots are used to display the relationship between two variables x and y. In this article, we’ll start by showing how to create beautiful scatter plots in R. We’ll use helper functions... [Read more]
TCGA癌症数据展示
By kassambara, The 31/08/2017 in ggpubr: Publication Ready Plots
Facilitating Exploratory Data Visualization: Application to TCGA Genomic Data
In genomic fields, it’s very common to explore the gene expression profile of one or a list of genes involved in a pathway of interest. Here, we present some helper functions in the ggpubr R... [Read more]
增加显著性标注
By kassambara, The 31/08/2017 in ggpubr: Publication Ready Plots
Add P-values and Significance Levels to ggplots
In this article, we’ll describe how to easily i) compare means of two or multiple groups; ii) and to automatically add p-values and significance levels to a ggplot (such as box plots, dot plots,... [Read more]
了解更多ggpur
用简单的函数即可对图形进行高度的定制，熟悉这些参数，然后调整自己的数据格式，绘制各种高级的图，R真是包罗万象
原始参考资料：
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