R语言中有很多程序包（package）可以做这个事情，包括limma, gplots, venneuler, 还有今天我们下面要介绍的VennDiagram包。各个工具用起来差别不是很大，可以根据个人喜好选择，不过其中limma包只能展示最多三个数据集的关系，后面三个包都可以展示超过三个数据集的维恩图。

1. 安装并加载包VennDiagram

> install.packages("VennDiagram")
> library(grid)
> library(VennDiagram)

2. 画维恩图的函数--venn.diagram()

VennDiagram包中画维恩图的函数是venn.diagram(). 下面我们来看一下venn.diagram()函数的使用及参数说明。

> 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, ...)

部分参数说明：

x: a list of vectors, e.g: list(A=1:10, B=3:8, C=5:13)
filename: 设置图形输出文件名
resolution: 输出图形的清晰度，DPI数值
imagetype: 输出图形的格式，tiff, png, svg 等
alpha: 设置每个区块的透明度
main: 图形标题
main.fontface: 字体样式，比如斜体，粗体等
main.fontfamily: 字体，比如Time New Roman等
关于调解文字的，不仅可以针对标题调节，还有参数分别针对子标题，维恩图中每个部分（类别）的名字进行字体，大小，和字体样式的设置。

更多关于venn.diagram函数的参数说明可以查看其详细文档
venn.diagram官网: Make a Venn Diagram in VennDiagram: Generate High-Resolution Venn and Euler Plots (rdrr.io)

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sample(x, size, replace=F) # 不放回抽样

二、venn基础图

1 两个圈

venn.diagram(
  x = list(set1, set2),
  category.names = c("Set 1" , "Set 2 "),
  filename = 'venn.png',
  output=TRUE
)

image

2 三个圈

venn.diagram(
  x = list(set1, set2, set3),
  category.names = c("Set 1" , "Set 2 " , "Set 3"),
  filename = 'venn.png',
  output=TRUE
)

image

3 四个圈

venn.diagram(
  x = list(set1, set2, set3, set4),
  category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4"),
  filename = 'venn.png',
  output=TRUE
)

image

4 五个圈

venn.diagram(
  x = list(set1, set2, set3, set4, set5),
  category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4", "Set 5"),
  filename = 'venn.png',
  output=TRUE
)

image

三、个性化参数调整

#调整参数进行图形优化

venn.plot <- draw.pairwise.venn(  area1 = 80,  #区域1的数 
area2 = 30,   #区域2的数 
cross.area = 2,  #重叠的个数 
category = c("First", "Second"),#分类命名
fill = c("blue", "red"),#1 2 区域分别的填充颜色 
lty = "blank",  #1 2 区域的边框线类型 
cex = 2,        #1 2 区域内部数字的字体大小 
cat.cex = 2,    # 分类名称的字体大小 
cat.dist = 0.09,   #分类名称距离边的距离 实际调整 
cat.just = list(c(-1, -1), c(1, 1)),  #分类名称的位置  ，圈内或者圈外
ext.pos = 30,  #线的角度 默认是正上方12点位置 
ext.dist = -0.05,   #外部线的距离  跟根据圆圈的大小适当调整
ext.length = 0.85,  #外部线长度 
ext.line.lwd = 2,  #外部线的宽度 
ext.line.lty = "dashed" )  #外部线为虚线);
grid.draw(venn.plot)

library(RColorBrewer)
color <- brewer.pal(3, "Set3")
# Chart
venn.diagram(
        x = list(set1, set2, set3),
        category.names = c("Set 1" , "Set 2 " , "Set 3"),
        filename = 'venn2.png',
        output=TRUE,

        # 输出
        imagetype="png" ,  # 类型（tiff png svg）
        #height = 1000 ,   # 高度
        #width = 1000 ,   # 宽度
        resolution = 400,  # 分辨率
        compression = "lzw",  # 压缩算法

        # 圈
        lwd = 5,  # 圈线条粗细 1 2 3 4 5
        lty = 1,  # 线条类型, 1 实线, 2 虚线, blank 无线条
        fill = color,  # 填充色
        col = c("red", 'green', 'blue'),  # 线条色

        # 数字 number
        cex = 2,  # 数字大小
        fontface = "bold",  # 加粗
        fontfamily = "sans",  # 字体

        # 标签 category
        cat.cex = 2,  # 字体大小
        cat.col = c("red", 'green', 'blue'),  # 字体色
        cat.fontface = "bold",  # 加粗
        cat.default.pos = "outer",  # 位置, outer 内 text 外
        cat.pos = c(-27, 27, 135),  # 位置，用圆的度数
        cat.dist = c(0.055, 0.055, 0.085),  # 位置，离圆的距离
        cat.fontfamily = "sans",  # 字体
        rotation = 1  # 1 2 3 旋转确定大打头数据集
)

image

四、保存

1 绘图待保存

library(RColorBrewer)

p = venn.diagram(
  x = list(set1, set2, set3, set4, set5),
  category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4", "Set 5"),
  # filename = 'venn.png',
  filename = NULL,
  output=TRUE,

  fill = brewer.pal(5, "Set2"),
  col = brewer.pal(5, "Set3"),
  fontface = "bold",
  cat.col = brewer.pal(5, "Set3"),
  cat.fontface = "bold"
)

2 保存为PDF

pdf("venn-pdf.pdf")
grid.draw(p)
dev.off()

image

3 保存为PNG

png("venn-png.png")
grid.draw(p)
dev.off()

image

更多参数：

col = NA  # 边框设为无色

参考：https://www.r-graph-gallery.com/14-venn-diagramm.html
venn网页工具：http://bioinformatics.psb.ugent.be/webtools/Venn/
venn.diagram函数文档: https://www.rdocumentation.org/packages/VennDiagram/versions/1.6.20/topics/venn.diagram
The R Graph Gallery绘图教程：https://www.r-graph-gallery.com/index.html
如何使用R来绘制韦恩图（Venn Diagram） - 云+社区 - 腾讯云 (tencent.com)