rm(list=ls())
library(ggplot2)
library(ggvenn)
library(paletteer)

if(!require(paletteer))install.packages("paletteer")

if(!require(scico))install.packages('scico')

if(!require(nord))install.packages('nord')

# 韦恩图的绘制学习

第一个韦恩图的画法

样例数据

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))

可视化绘制

opar <- par(family = "Roboto Condensed")
mypal= c('#E31A1CFF', '#FB9A99FF','#6A3D9AFF','#B2DF8AFF')##自定义颜色，选择paletteer的配色
ggvenn(a,
fill_color=mypal,#填充颜色
fill_alpha = .7,##调节透明度

   stroke_linetype = "longdash",#调节圈的线条样式：默认是"solid",这里我选择虚线
   stroke_color='white',#(线条颜色)：默认是"black"
   #stroke_alpha(线条透明度)：默认是1
   #stroke_size(线条宽度)：默认是1
   
   set_name_size = 8,#文本名大小
   #set_name_color = ,#(文本名颜色)：默认是"black" 
   text_size=5 #文本大小默认是4.
   ) 

可以在下面找到自己的配色

paletteer_c("scico::berlin", n = 10)

## <colors>

#9EB0FFFF #5AA3DAFF #2D7597FF #194155FF #11181DFF #270C01FF #501802FF #8A3F2AFF #C37469FF #FFACACFF

paletteer_d("RColorBrewer::Paired")

## <colors>

## #A6CEE3FF #1F78B4FF #B2DF8AFF #33A02CFF #FB9A99FF #E31A1CFF #FDBF6FFF #FF7F00FF #CAB2D6FF #6A3D9AFF #FFFF99FF #B15928FF

paletteer_dynamic("cartography::green.pal", 5)

## <colors>

## #B8D9A9FF #8DBC80FF #5D9D52FF #287A22FF #17692CFF

另一种韦恩图的画法

if(!require(VennDiagram))install.packages('VennDiagram')

library (VennDiagram)

A <- c("C", "D", "B", "E")

B <- c("C", "E", "B", "A")

C <- c("C", "E", "X", "Y")

venn.diagram(x= list(A = A,B = B,C = C),

filename = "pic.png",

height = 450, width = 450,

resolution =300,

imagetype="png",

col="transparent",

fill=c("green","yellow","darkorchid1"),

alpha = 0.50,

cex=0.45,

cat.cex=0.45)

#输入三个向量，最后一个参数是名字，根据实际情况修改

venn <- function(x,y,z,name,title){

if(!require(VennDiagram))install.packages('VennDiagram')

library (VennDiagram)

venn.diagram(x= list(Aff = x,Bio = y,Mine = z),

imagetype ="tiff",

filename=paste(name,".tiff"),

lwd=1,#圈线粗度

lty=1, #圈线类型

col=c('#0099CC','#FF6666','#FFCC99'), #圈线颜色

fill=c('#0099CC','#FF6666','#FFCC99'), #填充颜色

cat.col=c('#0099CC','#FF6666','#FFCC99'),#A和B的颜色

cat.cex = 1.5,# A和B的大小

rotation.degree = 0,#旋转角度

main = title,#主标题内容

main.cex = 1.5,#主标题大小

cex=1.5,#里面交集字的大小

alpha = 0.5,#透明度

reverse=TRUE)

}

venn(A,B,C)

BiocManager::install('ggVennDiagram')

BiocManager::install('hrbrthemes')

这个适合自己的个性化定制韦恩图

library(ggVennDiagram)

样例数据

genes <- paste("gene",1:1000,sep="")
set.seed(123)

随机抽取基因组成列表的四个元素

x <- list(A=sample(genes,300),
B=sample(genes,525),
C=sample(genes,440),
D=sample(genes,350))

可视化绘制

之后可以个性化定制自己需要的韦恩图

library(ggplot2)
ggVennDiagram(x, category.names = c("Stage 1","Stage 2","Stage 3", "Stage4"),
size=1,lty="longdash",color="gray60") +
scale_fill_gradient(name="Count",low="#EC7D85",high = "#182F6F") +
hrbrthemes::theme_ipsum(base_family = "sans") +
labs(title = "Example of ggVennDiagram:: ggVennDiagram function",
subtitle = "processed charts with ggVennDiagram()",
caption = "Visualization by DataCharm") +
theme(plot.title = element_text(hjust = 0.5,vjust = .5,color = "black",face = 'bold',
size = 20, margin = margin(t = 1, b = 12)),
plot.subtitle = element_text(hjust = 0,vjust = .5,size=15),
plot.caption = element_text(face = 'bold',size = 12),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank())

下面这个韦恩图函数有问题，会在getName报错，大家可以学习一下

# 需要这两个包 ggvenn、 export

library(grid)

library(ggvenn)

library(export)

venn <- function(..., Rplot = TRUE, PDF = NULL, PPT = NULL,

cex.label = 10, cex.num = 8,

alpha.fill = 0.7, col.fill = c("#E5D2DD", "#53A85F", "#F1BB72", "#F3B1A0"),

alpha.stroke = 1, size.stroke = 1,

col.stroke = "black",

show_percentage = FALSE

){

data_list = list(...)

names(data_list) = getName(...)

# build venn table

Len = length(data_list)

vennM = matrix("", Len, Len, dimnames = list(getName(...), getName(...)))

for(i in 1:Len){

for(j in i:Len){

vennM[i, j] = length(intersect(data_list[[i]], data_list[[j]]))

}

}

resM = apply(vennM, 1, as.numeric)

dimnames(resM) = dimnames(vennM)

if(Len > 4){

message("More than 4 objects, will not plot venn.")

return(resM)

}

# plot venn

require(ggvenn)

p <- suppressWarnings(ggvenn(

data = data_list,

show_percentage = show_percentage,

set_name_size = cex.label,

text_size = cex.num,

stroke_alpha = alpha.stroke,

stroke_size = size.stroke,

fill_alpha = alpha.fill,

fill_color = col.fill,

stroke_linetype = "longdash",

))

if(Rplot){

print(p)

}

if(!is.null(PDF)){

pdf(PDF, 8, 8)

print(p)

dev.off()

}

if(!is.null(PPT)){

require(export)

graph2ppt(p, file = PPT, width = 8, height = 8)

}

return(resM)

}

set.seed(123)

s1 = sample(LETTERS, 6)

s2 = sample(LETTERS, 8)

s3 = sample(LETTERS, 10)

s4 = sample(LETTERS, 12)

s5 = sample(LETTERS, 14)

venn(s1, s2, s3)

venn(s1, s2, s3, s4)

venn(s1, s2, s3, s4, s5)##五个以上的对象是建议花瓣图或者upset图

getAnywhere(getName)