定制小提琴图（Customising Violin Plots）_2020-02-10_M

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最新推荐文章于 2024-02-08 01:15:00 发布

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定制小提琴图（Customising Violin Plots）

# vioplot包测试_20200210Monday

## 1.设置当前工作目录

setwd("./vioplot/")

## 2.安装和导入R包：vioplot

# install.packages(vioplot)

library(vioplot)

# 载入需要的程辑包：sm

# Package 'sm', version 2.2-5.6: type help(sm) for summary information

# 载入需要的程辑包：zoo

# 载入程辑包：‘zoo’

# The following objects are masked from ‘package:base’:

# as.Date, as.Date.numeric

## 3.R包：vioplot简介

### 3.1 Description

# Package: vioplot

# Title: Violin Plot

# Version: 0.3.4

# Date: 2019-11-30

# Authors@R: c(person("Daniel", "Adler", email = "dadler@uni-goettingen.de", role = c("aut", "cph")),

# person("S. Thomas", "Kelly", email = "tom.kelly@riken.jp", role = c("aut", "cre")),

# person("Tom M.", "Elliott", email = "tom.elliott@auckland.ac.nz", role = c("ctb")))

# Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.

# Depends: sm, zoo

# License: BSD_3_clause + file LICENSE

# URL: https://github.com/TomKellyGenetics/vioplot

# BugReports: https://github.com/TomKellyGenetics/vioplot/issues

# LazyData: true

# RoxygenNote: 7.0.1

# Suggests: ggplot2, RColorBrewer, knitr, rmarkdown, testthat

# Language: en-GB

# VignetteBuilder: knitr

# Encoding: UTF-8

# NeedsCompilation: no

# Packaged: 2019-11-29 14:54:09 UTC; tom

# Author: Daniel Adler [aut, cph],

# S. Thomas Kelly [aut, cre],

# Tom M. Elliott [ctb]

# Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>

# Repository: CRAN

# Date/Publication: 2019-11-29 18:00:02 UTC

# Built: R 3.6.1; ; 2019-12-03 13:51:08 UTC; windows

### 3.2 Main function

ls(package:vioplot) # vioplot包中只有一个函数，说明这个函数中的参数可能有很多

# [1] "vioplot"

# Warning message:

# In ls(package:vioplot) : ‘package:vioplot’被转换成字符串

## 4.测试：Customising Violin Plots

#@ vioplot包是专门用来绘制小提琴图的R包，我们今天来测试一下它的功能和用法

#@ Therefore violin plots are a powerful tool to assist researchers to visualise data, particularly in the quality checking and exploratory parts of an analysis. Violin plots have many benefits:

# 1.Greater flexibility for plotting variation than boxplots

# 2.More familiarity to boxplot users than density plots

# 3.Easier to directly compare data types than existing plots

#@ 测试数据：鸢尾花数据iris

data("iris") # 载入R内置数据

class(iris) # 查看iris的数据集类型

# [1] "data.frame"

dim(iris) # 获取iris的数据维度信息

# [1] 150 5

head(iris) # 获取iris的前6行

# Sepal.Length Sepal.Width Petal.Length Petal.Width Species

# 1 5.1 3.5 1.4 0.2 setosa

# 2 4.9 3.0 1.4 0.2 setosa

# 3 4.7 3.2 1.3 0.2 setosa

# 4 4.6 3.1 1.5 0.2 setosa

# 5 5.0 3.6 1.4 0.2 setosa

# 6 5.4 3.9 1.7 0.4 setosa

str(iris) # 查看iris的数据集结构

# 'data.frame': 150 obs. of 5 variables:

# $ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...

# $ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...

# $ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...

# $ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...

# $ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

### 4.1 对比箱线图和小提琴图

#### 4.1.1 绘制箱线图

boxplot(iris$Sepal.Length[iris$Species == "setosa"], iris$Sepal.Length[iris$Species == "versicolor"], iris$Sepal.Length[iris$Species == "virginica"], names = c("setosa", "versicolor", "virginica"))

#### 4.1.2 绘制小提琴图

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"))

### 4.2 默认绘图

#@ 然而，正如我们在这里可以看到的，按照默认参数绘制出来的小提琴图是不美观的，一个相当显眼的颜色方案不适合专业或学术使用。因此，图片默认颜色效果如下：

### 4.3 图片颜色：小提琴的填充

#@ 图片的颜色可以用参数col进行自定义，举例如下：

#@ green vioplot

#@ blue vioplot

#@ brown vioplot

### 4.4 参数：向量化传参（Vectorisation）

#@ 上面的代码可以对小提琴图的颜色进行自定义，但还不够完美，如果可以用不同颜色可以去区别每个小提琴图的话那就更佳了，方法如下：

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"), main = "Sepal Length", col=c("lightgreen", "lightblue", "palevioletred")) # 同样还是对参数col进行调整，但是我们本次传入的参数是由三种颜色组成的向量，对应三个小提琴，分别对这三个小提琴图进行颜色填充

#@ 填加图例说明

legend("topleft", legend=c("setosa", "versicolor", "virginica"), fill=c("lightgreen", "lightblue", "palevioletred"), cex = 1) # 图例的位置、内容和字体大小都是可以灵活定制的，用到的函数是R基础函数：legend()

### 4.5 绘图颜色：小提琴线和箱线图

#@ 我们还可以用参数col和border对小提琴图的颜色填充和边界线颜色进行定制，举例如下：

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"), main = "Sepal Length", col="lightblue", border="royalblue") # 填充颜色：lightblue；边界颜色：royalblue(宝石蓝)

#@ 同样，参数lineCol和rectCol指定了boxplot轮廓和矩形填充的颜色。为了简单起见，盒子和盒图的胡须总是有相同的颜色(二者颜色由一个参数决定：lineCol)。用法举例如下：

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"), main = "Sepal Length", rectCol="lightblue", lineCol="violetred") # 设置参数lineCol，小提琴图的boxplot轮廓颜色为：violetred紫罗蓝色；设置参数rectCol，将boxplot填充颜色设置为：lightblue亮蓝色

#@ 同样的，通过参数colMed，我们还可以对中点的颜色进行设置。

### 4.6 整合vioplot的参数定制小提琴图

#@ 上面我们对vioplot的各个参数分别进行测试，现在我们将这些参数整合在一个vioplot函数中进行绘制，效果如下：

### 4.7 自定义小提琴中点的形状和颜色

#@ 不光可以对中点的颜色进行定制，还可以将中点设置为不同的形状，方法举例如下：

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"), main="Sepal Length (Equal Area)", areaEqual = T, col=c("lightgreen", "lightblue", "palevioletred"), border=c("darkolivegreen4", "royalblue4", "violetred4"), rectCol=c("forestgreen", "blue", "palevioletred3"), lineCol=c("darkolivegreen", "royalblue", "violetred4"), colMed=c("green", "cyan", "magenta"), pchMed=c(15, 17, 19)) # 参数colMed设置中点的颜色；参数pchMed设置中点的形状

### 4.8 优化参数定制美观的小提琴图

#@ 最后我们再加上图例和对每个小提琴进行不同颜色区别的参数，定制美观的小提琴图

vioplot(iris$Sepal.Length[iris$Species=="setosa"], iris$Sepal.Length[iris$Species=="versicolor"], iris$Sepal.Length[iris$Species=="virginica"], names=c("setosa", "versicolor", "virginica"), main="Sepal Length (Equal Area)", areaEqual = T, col=c("lightgreen", "lightblue", "palevioletred"), border=c("darkolivegreen4", "royalblue4", "violetred4"), rectCol=c("forestgreen", "blue", "palevioletred3"), lineCol=c("darkolivegreen", "royalblue", "violetred4"), colMed=c("green", "cyan", "magenta"), pchMed=c(15, 17, 19)) # 绘制小提琴图

legend("topleft", legend=c("setosa", "versicolor", "virginica"), fill=c("lightgreen", "lightblue", "palevioletred"), cex = 1) # 填加图例

## 5.结束

sessionInfo()

# R version 3.6.2 (2019-12-12)

# Platform: x86_64-w64-mingw32/x64 (64-bit)

# Running under: Windows 10 x64 (build 18363)

# Matrix products: default

# locale:

# [1] LC_COLLATE=Chinese (Simplified)_China.936

# [2] LC_CTYPE=Chinese (Simplified)_China.936

# [3] LC_MONETARY=Chinese (Simplified)_China.936

# [4] LC_NUMERIC=C

# [5] LC_TIME=Chinese (Simplified)_China.936

# attached base packages:

# [1] stats graphics grDevices utils datasets methods

# [7] base

# other attached packages:

# [1] vioplot_0.3.4 zoo_1.8-7 sm_2.2-5.6

# loaded via a namespace (and not attached):

# [1] compiler_3.6.2 tools_3.6.2 grid_3.6.2

# [4] packrat_0.5.0 lattice_0.20-38 tcltk_3.6.2

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定制小提琴图（Customising Violin Plots）_2020-02-10_M

定制小提琴图（Customising Violin Plots）# vioplot包测试_20200210Monday## 1.设置当前工作目录setwd("./vioplot/")## 2.安装和导入R包：vioplot# install.packages(vioplot)library(vioplot)# 载入需要的程辑包：sm# Package '...
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