ggpubr: 'ggplot2' Based Publication Ready Plots

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.

Installation and loading

• 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")

Geting started

Find out more at http://www.sthda.com/english/rpkgs/ggpubr.

Density and histogram plots

library(ggpubr)
#> Loading required package: ggplot2
# 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"))

# 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"))

Box plots and violin plots

# 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
 ggboxplot(df, x = "dose", y = "len",
    color = "dose", palette =c("#00AFBB", "#E7B800", "#FC4E07"),
    add = "jitter", shape = "dose")

 
# 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"))

More

Find out more at http://www.sthda.com/english/rpkgs/ggpubr.

Blog posts

• A. Kassambara. STHDA Jully 2016. ggpubr R Package: ggplot2-Based Publication Ready Plots