画韦恩图，常见的如下。
image.png
image.png
对于已经司空见惯的veen图，审稿人也是审美疲劳了。那就换一个让他眼前一亮的veen图。
image.png
image.png
目前数据不完善，计划做6元Veen图。数据没凑齐，暂时不做。
参考链接1
参考链接2
参考链接3
参考链接4
常见的R包比如gplots、venneuler、VennDiagram等最多只能画5元。
R包venn，它能绘制6元、7元韦恩图。
R包UpSetR,是做出上述点线图格式的工具。
#演示数据
install.packages("UpSetR")
library("UpSetR")
require(ggplot2); require(plyr); require(gridExtra); require(grid);
movies <- read.csv(system.file("extdata","movies.csv",package = "UpSetR"), header = TRUE, sep=";")
upset(movies, nsets = 7, nintersects = 30, mb.ratio = c(0.5, 0.5),
order.by = c("freq", "degree"), decreasing = c(TRUE,FALSE))
image.png
常规韦恩图使用VennDiagram包。
三元韦恩图
m17 <- read.csv("m17_4g.dsg2.csv")
e28 <- read.csv("e28_4g.dsg2.csv")
m17_e28 <- read.csv("m17_e28_deg.csv",header = TRUE)
m17 <- as.vector(unlist(m17[1]))
e28 <- as.vector(unlist(e28[1]))
m17_e28 <- as.vector(unlist(m17_e28[1]))
#主要是获取对应的差异表达基因，转换成向量。
#veen.diagram中变量名称不能使用-,否则会报错。变量名要求是字母开头。
venn.plot <- venn.diagram(
x = list(
Mo17_DY13 = m17, #对应三个元的，前面是图中显示字符，后面是实际变量
E28_DY13 = e28,
Mo17_E28 = m17_e28
),
filename = "DY13.tiff", #输出的文件名
col = "transparent",
fill = c("red", "blue", "green"), #各个圈圈的颜色
alpha = 0.5, #透明度
label.col = c("darkred", "white", "darkblue", "white",
"white", "white", "darkgreen"),
cex = 2.5,
fontfamily = "serif",
fontface = "bold",
cat.default.pos = "text", #此处默认是标签在圆内部
cat.col = c("darkred", "darkblue", "darkgreen"),
cat.cex = 2.5,
cat.fontfamily = "serif",
cat.dist = c(0.06, 0.06, 0.03),
cat.pos = 0
)
标签在圆内部的三元韦恩图
标签在圆圈外面的代码
venn.plot <- venn.diagram(
x = list(
Mo17_DY13 = m17,
E28_DY13 = e28,
Mo17_E28 = m17_e28
),
filename = "DY13.tiff",
col = "transparent",
fill = c("red", "blue", "green"),
alpha = 0.5,
label.col = c("darkred", "white", "darkblue", "white",
"white", "white", "darkgreen"),
cex = 2.5,#内标签的字体大小
fontfamily = "serif",
fontface = "bold",
cat.default.pos = "outer",#设置标签在圆外面
#cat.col = c("darkred", "darkblue", "darkgreen"),
cat.cex = 2,#外标签的字体大小
cat.fontfamily = "serif",
cat.dist = c(0.05, 0.05, 0.05),#相对圆圈的位置
cat.pos = c(-20,20,180) #相对12点方向旋转的角度
)
标签在圆外面的三元韦恩图
