Violin Group

Authors

[Editor] Hu Zheng;

[Contributors]

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Violin Group plugin. You can also use the Hiplot website to achieve no code ploting. For more information please see the following link:

https://hiplot.cn/basic/violin-group?lang=en

Violin and box plot of grouped data with T-test.

Setup

  • System Requirements: Cross-platform (Linux/MacOS/Windows)

  • Programming language: R

  • Dependent packages: data.table; jsonlite; ggpubr; ggthemes

# Install packages
if (!requireNamespace("data.table", quietly = TRUE)) {
  install.packages("data.table")
}
if (!requireNamespace("jsonlite", quietly = TRUE)) {
  install.packages("jsonlite")
}
if (!requireNamespace("ggpubr", quietly = TRUE)) {
  install.packages("ggpubr")
}
if (!requireNamespace("ggthemes", quietly = TRUE)) {
  install.packages("ggthemes")
}

# Load packages
library(data.table)
library(jsonlite)
library(ggpubr)
library(ggthemes)

Data Preparation

  • <1st-col>: (Numeric) value data
  • <2nd-col>: (String) 1st-rank groups
  • <3rd-col>: (String) 2nd-rank groups
# Load data
data <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/violin-group/data.json")$exampleData$textarea[[1]])
data <- as.data.frame(data)

# convert data structure
data[, 3] <- factor(data[, 3], levels = unique(data[, 3]))

# View data
head(data)
  Value Group1 Group2
1   4.2    low treat1
2  11.5    low treat1
3   7.3    low treat1
4   5.8    low treat1
5   6.4    low treat1
6  10.0    low treat1

Visualization

# Violin Group
p <- ggviolin(data, x = "Group1", y = "Value", color = "Group2", add = "dotplot",
              add.params = list(fill = "white",size = 1), title = "Violin Diagram",
              xlab = "Group1", ylab = "Value", fill = "Group2",
              palette = c("#374E55FF", "#DF8F44FF"), alpha = 0.5, trim = F) +
  stat_compare_means(aes(group = data[, colnames(data)[3]]),
    method = "t.test", vjust = -6, label.x.npc = "left", label.y.npc = "top",
    tip.length = 0.03, bracket.size = 0.3, step.increase = 0, position = "identity",
    na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, geom = "text") +
  theme_stata() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12,hjust = 0.5),
        axis.title = element_text(size = 12),
        axis.text = element_text(size = 10),
        axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p
FigureΒ 1: Violin Group