R语言绘图包05--韦恩图的绘制：ggvenn和VennDiagram

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R语言绘图包系列：

• R语言绘图包01--优秀的拼图包patchwork
• R语言绘图包02--热图pheatmap
• R语言绘图包03--火山图EnhancedVolcano
• R语言绘图包04--GOplot：富集分析结果可视化

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韦恩图可以用来展示各个数据集之间的重叠关系
绘制韦恩图的方法很多，在这里介绍两种
1. ggvenn绘制韦恩图
2. 使用VennDiagram函数包中的venn.diagram函数绘制韦恩图

1. ggvenn

这个包支持列表或数据框的数据作为输入

install.packages("devtools")
devtools::install_github("yanlinlin82/ggvenn")

1.1 输入list

library(ggvenn)
library(patchwork)
a <- list(`Set 1` = c(1, 3, 5, 7, 9),
          `Set 2` = c(1, 5, 9, 13),
          `Set 3` = c(1, 2, 8, 9),
          `Set 4` = c(6, 7, 10, 12))
p1=ggvenn(a, c("Set 1", "Set 2"))            # draw two-set venn
p2=ggvenn(a, c("Set 1", "Set 2", "Set 3"))   # draw three-set venn
p3=ggvenn(a)   # without set names, the first 4 elements in list will be chose to draw four-set venn
p1|p2|p3

1.2 输入数据框（每个列是一个set）

d <- tibble(value   = c(1,     2,     3,     5,     6,     7,     8,     9),
            `Set 1` = c(TRUE,  FALSE, TRUE,  TRUE,  FALSE, TRUE,  FALSE, TRUE),
            `Set 2` = c(TRUE,  FALSE, FALSE, TRUE,  FALSE, FALSE, FALSE, TRUE),
            `Set 3` = c(TRUE,  TRUE,  FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE),
            `Set 4` = c(FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE,  FALSE, FALSE))
p1=ggvenn(d, c("Set 1", "Set 2"))           # draw two-set venn
p2=ggvenn(d, c("Set 1", "Set 2", "Set 3"))  # draw three-set venn
p3=ggvenn(d)   # without set names, the first 4 logical column in data.frame will be chose to draw four-set venn
p1|p2|p3

1.3 数据框作为输入时，还可以使用ggplot2的语法绘制

# draw two-set venn (use A, B in aes)
p1=ggplot(d, aes(A = `Set 1`, B = `Set 2`)) +
  geom_venn() + theme_void() + coord_fixed()
# draw three-set venn (use A, B, C in aes)
p2=ggplot(d, aes(A = `Set 1`, B = `Set 2`, C = `Set 3`)) +
  geom_venn() + theme_void() + coord_fixed()
# draw four-set venn (use A, B, C, D in aes)
p3=ggplot(d, aes(A = `Set 1`, B = `Set 2`, C = `Set 3`, D = `Set 4`)) +
  geom_venn() + theme_void() + coord_fixed()
p1|p2|p3

1.4 美化

1.4.1 美化颜色和大小

颜色填充参数：
fill_color - 默认是 c("blue", "yellow", "green", "red")
fill_alpha - 默认是 0.5
边线设置参数:
stroke_color - 默认是 "black"
stroke_alpha - 默认是 1
stroke_size - 默认是 1
stroke_linetype - 默认是 "solid"
集合名字设置:
set_name_color - 默认是 "black"
set_name_size - 默认是 6
图形中字体设置:
text_color - 默认是 "black"
text_size - 默认是 4
以上所有的参数都可以用于ggvenn() 和 geom_venn()

# For example:
a <- list(A = 1:4, B = c(1,3,5))
ggvenn(a, stroke_linetype = 2, stroke_size = 0.5,
  set_name_color = "red", set_name_size = 15,
  fill_color = c("pink", "gold"))

1.4.2 展示元素
show_elements - 默认是 FALSE
label_sep - text used to concatenate elements, default is ","

#For example:
a <- list(A = c("apple", "pear", "peach"),
          B = c("apple", "lemon"))
p1=ggvenn(a, show_elements = TRUE)
p2=ggvenn(a, show_elements = TRUE, label_sep = "\n")  # show elements in line
p1|p2

1.4.3 隐藏百分比，改变百分比的小数点位数
show_percentage - 默认是TRUE
digits - 默认是 1

a <- list(A = 1:5, B = 1:2)
p1=ggvenn(a, show_percentage = FALSE)
p2=ggvenn(a, digits = 2)
p1|p2

2. venn.diagram

参数：

venn.diagram(x, filename, height = 3000, width = 3000, resolution =
    500, imagetype = "tiff", units = "px", compression =
    "lzw", na = "stop", main = NULL, sub = NULL, main.pos
    = c(0.5, 1.05), main.fontface = "plain",
    main.fontfamily = "serif", main.col = "black",
    main.cex = 1, main.just = c(0.5, 1), sub.pos = c(0.5,
    1.05), sub.fontface = "plain", sub.fontfamily =
    "serif", sub.col = "black", sub.cex = 1, sub.just =
    c(0.5, 1), category.names = names(x), force.unique =
    TRUE, print.mode = "raw", sigdigs = 3, direct.area =
    FALSE, area.vector = 0, hyper.test = FALSE, total.population = NULL, 
    lower.tail = TRUE, ...)

2.1 绘制一张最基本的韦恩图

library(VennDiagram)
# 生成数据集
set1 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")
set2 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")
set3 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")

venn.diagram(
  x = list(set1, set2, set3),
  category.names = c("Set 1" , "Set 2 " , "Set 3"),
  filename = 'venn_diagramm.png',
  output=TRUE) #直接在工作目录下生成这个名为venn_diagramm.png的图像

2.2 添加颜色

library(RColorBrewer)
myCol <- brewer.pal(3, "Pastel2")
venn.diagram(
        x = list(set1, set2, set3),
        category.names = c("Set 1" , "Set 2 " , "Set 3"),
        filename = 'venn_diagramm_color.png',
        output=TRUE,

        # Output features
        imagetype="png" ,
        height = 480 , 
        width = 480 , 
        resolution = 300,
        compression = "lzw",

        # Circles
        lwd = 2,
        lty = 'blank',
        fill = myCol,

        # Numbers
        cex = .6,
        fontface = "bold",
        fontfamily = "sans",

        # Set names
        cat.cex = 0.6,
        cat.fontface = "bold",
        cat.default.pos = "outer",
        cat.pos = c(-27, 27, 135),
        cat.dist = c(0.055, 0.055, 0.085),
        cat.fontfamily = "sans",
        rotation = 1
)

2.3 更改样式

# Libraries
library(tidyverse)
library(hrbrthemes)
library(tm)
library(proustr)
library(VennDiagram)

#数据准备
data <- read.table("https://raw.githubusercontent.com/holtzy/data_to_viz/master/Example_dataset/14_SeveralIndepLists.csv", header=TRUE) 
to_remove <- c("_|[0-9]|\\.|function|^id|script|var|div|null|typeof|opts|if|^r$|undefined|false|loaded|true|settimeout|eval|else|artist")
data <- data %>% filter(!grepl(to_remove, word)) %>% filter(!word %in% stopwords('fr')) %>% filter(!word %in% proust_stopwords()$word)


# 绘图
venn.diagram(
    x = list(
        data %>% filter(artist=="booba") %>% select(word) %>% unlist() , 
        data %>% filter(artist=="nekfeu") %>% select(word) %>% unlist() , 
        data %>% filter(artist=="georges-brassens") %>% select(word) %>% unlist()
    ),
    category.names = c("Booba (1995)" , "Nekfeu (663)" , "Brassens (471)"),
    filename = 'venn.png',
    output = TRUE ,
    imagetype="png" ,
    height = 480 , 
    width = 480 , 
    resolution = 300,
    compression = "lzw",
    lwd = 1,
    col=c("#440154ff", '#21908dff', '#fde725ff'),
    fill = c(alpha("#440154ff",0.3), alpha('#21908dff',0.3), alpha('#fde725ff',0.3)),
    cex = 0.5,
    fontfamily = "sans",
    cat.cex = 0.3,
    cat.default.pos = "outer",
    cat.pos = c(-27, 27, 135),
    cat.dist = c(0.055, 0.055, 0.085),
    cat.fontfamily = "sans",
    cat.col = c("#440154ff", '#21908dff', '#fde725ff'),
    rotation = 1
)

VennDiagram函数包最大能绘制5个数据集合的韦恩图。

参考：
https://github.com/yanlinlin82/ggvenn
R语言画维恩图--ggvenn
venn.diagram函数文档
The R Graph Gallery绘图教程
https://cloud.tencent.com/developer/article/1675092
https://www.jianshu.com/p/f858521828a5