（23）用R做花瓣图和在线网站upset图

琉璃月月呀

已于 2024-03-25 09:58:25 修改

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文章标签： r语言数据库服务器

于 2023-12-12 16:03:55 首次发布

本文链接：https://blog.csdn.net/weixin_44562189/article/details/134952061

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一、用R做花瓣图

注！！！先把前面数据都导入进去之后再生成花瓣图，现在已经更新了3、4、5三个版本，注意文件名的对应，然后导出的时候选择PDF，选择A4格式导出

#做花瓣Venn图，目的是统计一下现在得到的正选择结果有多少重复的和特异性的，用R做
#设置工作目录
setwd(dir = "C:/Users/Lenovo/Desktop/repeat")
# 导入所需的包
library(grid)
library(futile.logger)
library(VennDiagram)
library(venn)
library(ggplot2)
# 读取文件中的基因列表
#我这次有5个文件，引号中是文件名，就是先把这些数据导入进去
genes1 <- read.table("branchsite_all.txt", header = FALSE, col.names = "Gene")
genes2 <- read.table("site_m1m2_all.txt", header = FALSE, col.names = "Gene")
genes3 <- read.table("site_m7m8_1368.txt", header = FALSE, col.names = "Gene")
genes4 <- read.table("site_m7m8_all.txt", header = FALSE, col.names = "Gene")
genes5 <- read.table("w999_quickevolution.txt", header = FALSE, col.names = "Gene")
# 将基因列表转换为字符向量，这样我5个文件就转换成了5个字符向量，下面就用genesX代替
genes1 <- as.character(genes1$Gene)
genes2 <- as.character(genes2$Gene)
genes3 <- as.character(genes3$Gene)
genes4 <- as.character(genes4$Gene)
genes5 <- as.character(genes5$Gene)
 # 生成花瓣图，这个会分别计算5个中两两之间、三个、四个、五个的重叠度，注意category那里要填写一下文件名称，其他地方无需改动
venn.plot <- draw.quintuple.venn(
  area1 = length(genes1),
  area2 = length(genes2),
  area3 = length(genes3),
  area4 = length(genes4),
  area5 = length(genes5),
  n12 = length(intersect(genes1, genes2)),
  n13 = length(intersect(genes1, genes3)),
  n14 = length(intersect(genes1, genes4)),
  n15 = length(intersect(genes1, genes5)),
  n23 = length(intersect(genes2, genes3)),
  n24 = length(intersect(genes2, genes4)),
  n25 = length(intersect(genes2, genes5)),
  n34 = length(intersect(genes3, genes4)),
  n35 = length(intersect(genes3, genes5)),
  n45 = length(intersect(genes4, genes5)),
  n123 = length(intersect(intersect(genes1, genes2), genes3)),
  n124 = length(intersect(intersect(genes1, genes2), genes4)),
  n125 = length(intersect(intersect(genes1, genes2), genes5)),
  n134 = length(intersect(intersect(genes1, genes3), genes4)),
  n135 = length(intersect(intersect(genes1, genes3), genes5)),
  n145 = length(intersect(intersect(genes1, genes4), genes5)),
  n234 = length(intersect(intersect(genes2, genes3), genes4)),
  n235 = length(intersect(intersect(genes2, genes3), genes5)),
  n245 = length(intersect(intersect(genes2, genes4), genes5)),
  n345 = length(intersect(intersect(genes3, genes4), genes5)),
  n1234 = length(intersect(intersect(intersect(genes1, genes2), genes3), genes4)),
  n1235 = length(intersect(intersect(intersect(genes1, genes2), genes3), genes5)),
  n1245 = length(intersect(intersect(intersect(genes1, genes2), genes4), genes5)),
  n1345 = length(intersect(intersect(intersect(genes1, genes3), genes4), genes5)),
  n2345 = length(intersect(intersect(intersect(genes2, genes3), genes4), genes5)),
  n12345 = length(intersect(intersect(intersect(intersect(genes1, genes2), genes3), genes4), genes5)),
  category = c("branchsite_all.txt", "site_m1m2_all.txt", "site_m7m8_1368.txt", "site_m7m8_all.txt", "w999_quickevolution.txt"),
  fill = c("skyblue", "pink", "lightgreen", "orange", "purple"),  # 添加新颜色选项
  lty = "blank",
  cex = 1.2,
  fontface = "bold",
  fontfamily = "sans"
)

###以下是生成3个文件的花瓣图的代码，下面的genes1,2,4是指上文中1,2,4文件，这个都可以自己定义
# 生成花瓣图
venn.plot <- draw.triple.venn(
  area1 = length(genes1),
  area2 = length(genes2),
  area3 = length(genes4),
  n12 = length(intersect(genes1, genes2)),
  n23 = length(intersect(genes2, genes4)),
  n13 = length(intersect(genes1, genes4)),
  n123 = length(intersect(intersect(genes1, genes2), genes4)),
  category = c("branchsite_all.txt", "site_m1m2_all.txt", "site_m7m8_all.txt"),
  fill = c("skyblue", "pink", "lightgreen"),
  lty = "blank",
  cex = 1.2,
  fontface = "bold",
  fontfamily = "sans"
)