Analysis in R: ggplot2 made easy! The “ggpubr” package

公開日 2023-01-25

Although ggplot2 is a useful package for plotting data, sometimes the procedures for doing so can be cumbersome. However, this package can solve such problems.

The following is a list of commands that are likely to be used frequently from the commands included in the package. For other commands, see the package help. Duplicate command options are omitted.

Package version is 0.4.0. Checked with R version 4.2.2.

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Install Package

Run the following command.

#Install Package
install.packages("ggpubr")

Examples

See the command and package help for details.

#Loading the library
library("ggpubr")

###Creating Data Examples#####
n <- 100
TestData <- data.frame("Group" = factor(rep(c("Group1", "Group2", "Group3", "Group4"), each = 25)),
                          "Data" = c(rnorm(25, 10), rnorm(25, 15), rnorm(25, 20), rnorm(25, 25)))
########

#Create density plot:ggdensity command
#Data:data option
#x-axis data:x option
#y-axis data:y option;"..density..","..count.."
#Line color:color option;Default is "black"
#Fill color:fill option;Default is NA
#Color pallet:palette option;"ggsci package":"npg","aaas",
#"lancet","jco","ucscgb","uchicago","simpsons","rickandmorty"
#Line type:linetype option;"twodash","longdash","dotdash","dotted",
#"dashed","solid","blank"
#Fill color transparency:alpha option;Default is 0.5
#Adding information to the plot:add option;"none","mean","median"
#Line type for add option:add.params option;Use list class
#Add lag plot:rug option;Default is FALSE
ggdensity(data = TestData, x = "Data", y = "..count..",
          color = "Group", fill = "Group", palette = "lancet",
          linetype = "solid", alpha = 0.3, add = "mean",
          add.params = list(linetype = "dashed"), rug = TRUE, main = "TEST")

#Create Box plot:ggboxplot command
#Make a notched box plot:notch option;TRUE/FALSE
#Adding information to the plot:add option;"none","dotplot","jitter",
##"mean","mean_se","mean_sd","mean_ci","mean_range",
##"median","median_iqr","median_mad","median_range"
ggboxplot(data = TestData, x = "Group", y = "Data",
          color = "Group", size = 0.5, width = 1,
          notch = FALSE, palette = "lancet",
          add = "jitter", add.params = list(color = "blue", size = 0.5),
          main = "TEST")

#Create pie chart:ggpie command
#Location of data labels:lab.pos option;in/out
#Data Label Format:lab.font option:set a c(size, style, color)
#Ignored when lab.pos option is out
#Examples
PieData <- data.frame(Group = c("Data1", "Data2", "Data3"),
                         Value = c(25, 25, 50))
ggpie(data = PieData, x = "Value", label = "Value", lab.pos = "in",
      lab.font = c(15, "bold", "white"), color = "black",
      fill = "Group", palette = "lancet", size = 1, main = "TEST")

#Create Violon plot:ggviolin command
ggviolin(data = TestData, x = "Group", y = "Data",
         fill = "Group", size = 0.5, width = 1,
         palette = "lancet", add = "boxplot",
         add.params = list(fill = "white"), main = "TEST")