Fig2-b VennDiagram绘制Venn图 2020-1

3.5 Venn Diagram Venn图的绘制：三维和四维Venn图的绘制
Venn图是可以表示某个值在不同组中的交集和并集关系，因此可以是数值、字符串（即文字）类的相互重叠和不重叠部分的展示。

3.5.1 三维Venn图的绘制：
数据格式：

image.png

install.packages('VennDiagram')#安装包
library(VennDiagram)#导入包
sdv<-read.csv(file.choose())#读取数据

三维Venn图的绘制：

sdv.plot <- venn.diagram(
    x = list( Pyloric.caeca=sdv$Pyloric.caeca, Midgut = sdv$Midgut, Hindgut = sdv$Hindgut),
    filename = 'C:/Users/Mr.R/Documents/ReproduceImages/Reproduction1 Core gut microbial communities are maintained by beneficial interactions and strain/sdvVennDiagram.tiff',    
    col = "black", lwd = 1,
    fill = c("cornflowerblue", "green", "yellow"),alpha = 0.20, cex = 0.6,    fontfamily = "serif",    fontface = "bold",  cat.col = c("darkblue", "darkgreen", "orange"), cat.cex = 1.2,    
    cat.fontface = "bold",cat.fontfamily = "serif")

得到的结果为： image.png

3.5.2 四维Venn图的绘制
1）数据格式为：

image.png

首先安装对应的包并加载

install.packages('VennDiagram')#安装包
library(VennDiagram)#导入包

读取数据

vn= read.table('C:/Users/Mr.R/Documents/ReproduceImages/Reproduction1 Core gut microbial communities are maintained by beneficial interactions and strain/venn.txt', header = T,sep="\t")
head(vn)#显示数值首6行

image.png

开始作图：

venn.plot <- venn.diagram(
x = list( High.marine.Protein= vn$High.marine.Protein, Medium.fat = vn$Medium.fat, High.fat = vn$High.fat,  Low.marine.protein = vn$Low.marine.protein    ),
filename = 'C:/Users/Mr.R/Documents/ReproduceImages/Reproduction1 Core gut microbial communities are maintained by beneficial interactions and strain/VennDiagram1.tiff',    
col = "black",    lty = "dotted",lwd = 1,
fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),alpha = 0.20,    
label.col = c("orange", "white", "darkorchid4", "white", "white", "white","white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"),
cex = 0.6,    fontfamily = "serif",    fontface = "bold",    
cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"), cat.cex = 0.6,    
cat.fontface = "bold",cat.fontfamily = "serif")

得到以下图形：

image.png

说明：

x = list( High.marine.Protein= vn$High.marine.Protein, Medium.fat = vn$Medium.fat, High.fat = vn$High.fat,  Low.marine.protein = vn$Low.marine.protein    ),#形成list
filename = 'C:/Users/Mr.R/Documents/ReproduceImages/Reproduction1 Core gut microbial communities are maintained by beneficial interactions and strain/VennDiagram1.tiff', #输出位置和图片格式
   col = "black",    lty = "dotted", #边框线型为"dotted"可以得到虚线，如果不赋值会默认实现
   lwd = 1, # 边框线的宽度
 fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),   alpha = 0.20,    #对不同组的着色
label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white",white", "white", "white", "darkgreen", "white"),#是对交集元素个数的数字的颜色
cex = 1.0,  fontfamily = "serif",    fontface = "bold",    cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),    #字体粗细和颜色等
cat.cex = 0.8, cat.fontface = "bold",#标记文字的字体大小和粗细
 cat.fontfamily = "serif")

但是原图是实现，数字标记为黑色，所以稍加修改：去掉虚线线性，去掉数字标记颜色，默认使用黑色实现。

venn.plot <- venn.diagram(
    x = list( High.marine.Protein= vn$High.marine.Protein, Medium.fat = vn$Medium.fat, High.fat = vn$High.fat,  Low.marine.protein = vn$Low.marine.protein    ),
    filename = 'C:/Users/Mr.R/Documents/ReproduceImages/Reproduction1 Core gut microbial communities are maintained by beneficial interactions and strain/VennDiagram.tiff',    
    col = "black",    ,lwd = 1,
    fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),alpha = 0.20,    
    cex = 0.6,    fontfamily = "serif",    fontface = "bold",    
    cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"), cat.cex = 0.6,    
    cat.fontface = "bold",cat.fontfamily = "serif")

得到最终结果

image.png