韦恩图还有这个功能。:可以导出Excel表格 venn

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生信小博士

发布于 2024-02-23 23:21:58

1490

发布于 2024-02-23 23:21:58

文章被收录于专栏：单细胞单细胞

主要是本文代码还可以出venn图的excel表格，在文末。

大家好，是不是有时候你画韦恩图的网页工具画出来的图特别丑，就像这样，标签都看不到，或者在圆圈里面：

输入数据

假如我们有三个list，或者向量、数据框也可以，list内容分别是m6a-seq的差异基因，RIP-seq的差异基因和 genecards中的你的目的基因集

gene_cards <- data.frame(`Gene Symbol` = c("BRCA1", "TP53", "EGFR", "ERBB2", "KRAS", "BRAF", "ALK", "RET", "ROS1"),                         `Gene Description` = c("Breast cancer 1", "Tumor protein p53", "Epidermal growth factor receptor", "Erb-B2 receptor tyrosine kinase 2", "Kirsten rat sarcoma viral oncogene homolog", "B-Raf proto-oncogene, serine/threonine kinase", "Anaplastic lymphoma receptor tyrosine kinase", "Ret proto-oncogene", "ROS proto-oncogene 1, receptor tyrosine kinase"),                         stringsAsFactors = FALSE)Rip_seq <- c("BRCA1", "TP53", "EGFR", "AKT1", "MTOR", "CCND1", "MYC")m6A_seq <- c("BRCA1", "TP53", "EGFR", "ERBB2", "KRAS", "BRAF", "AKT1", "MTOR", "CCND1", "MYC")genecards_intersect_with_m6a_rip <- Reduce(intersect, list(gene_cards$`Gene.Symbol`, Rip_seq, m6A_seq))print(genecards_intersect_with_m6a_rip)

把输入数据变成list，绘制韦恩图

VennDiagram要求的输入数据就是list

# 韦恩图library(VennDiagram)venn_list <- list('Genecards' = gene_cards$`Gene.Symbol`,                  'm6A_seq' = m6A_seq, 'Rip_seq' = Rip_seq)venn_listvenn.diagram(venn_list, filename = 'venn2.png', imagetype = 'png',              fill = c('red', 'blue','green'), alpha = 0.30,             #cat.col = rep('black', 3),              # col = 'black',                          cex = 1.5,  # 设置文本标签大小             fontfamily = "serif",  # 设置文本标签的字体             fontface = "bold",  # 设置文本标签的字体加粗             cat.col = c("red", "darkblue", "darkgreen"  ),  # 设置类别标签的颜色             cat.cex = 1   ,  # 设置类别标签大小             # cat.pos = 0,  # 设置类别标签的位置             cat.pos = c(-60,60,180) , # 设置类别标签的位置 (1,2,3,4,5  numeric  Vector giving the position (in degrees) of each category name along the circle, with 0 at 12 o'clock)             margin  = 0.08  #调整标签距离最边缘的位置             )

输出韦恩图的excel表格

这个excel可以放在你的补充材料里，知道不同集合交集的结果是什么

inter <- get.venn.partitions(venn_list)for (i in 1:nrow(inter)) inter[i,'values'] <- paste(inter[[i,'..values..']], collapse = ', ')#write.table(inter[-c(5, 6)] , 'venn_inter.txt', row.names = FALSE, sep = '\t', quote = FALSE)for (i in 1:nrow(inter)) inter[i,'values'] <- paste(inter[[i,'..values..']], collapse = ', ')openxlsx::write.xlsx(inter[-c(5, 6)], 'venn_inter.xlsx', row.names = FALSE, sep = ',', quote = FALSE)