英文:
Extract values from each region of a venn diagram
问题
我有6个列表。每个列表都包含特定状况下感兴趣的基因。然后使用这六个列表在R中使用venn包制作了一个Venn图。
这个Venn图正是我想要的，但现在我想生成一个包含Venn图中每个部分基因的列表。我该怎么做？即如何找出我的列表中构成每个列表/条件中存在的1251个基因的基因？
library(venn)venn_list_no <- list(pt_v_lb = rownames(pt_v_lb_no), lbdm_v_lb = rownames(lbdm_v_lb_no), ptdm_v_lb = rownames(ptdm_v_lb_no), lbdm_v_pt = rownames(lbdm_v_pt_no), ptdm_v_pt = rownames(ptdm_v_pt_no), ptdm_v_lbdm = rownames(ptdm_v_lbdm_no))venn(venn_list_no, zcolor = "style", ggplot = T, opacity = 0.2, box = F)+theme()
英文:
I have 6 lists. Each contains genes of interest from a given condition. These six lists were then used to make a venn diagram in r using the venn package.
The venn diagram is precisely what I want, but now I would like to produce a list of genes from each section of the venn diagram. how do I do this? i.e. how do I figure out what genes from my lists comprise the 1251 genes that are present in each list/condition?
library(venn)venn_list_no <- list(pt_v_lb = rownames(pt_v_lb_no), lbdm_v_lb = rownames(lbdm_v_lb_no), ptdm_v_lb = rownames(ptdm_v_lb_no), lbdm_v_pt = rownames(lbdm_v_pt_no), ptdm_v_pt = rownames(ptdm_v_pt_no), ptdm_v_lbdm = rownames(ptdm_v_lbdm_no))venn(venn_list_no, zcolor = "style", ggplot = T, opacity = 0.2, box = F)+theme()
答案1
得分: 0
我查看了包的源代码，但我找不到任何文档化的用于提取区域元素的函数。实际上，venn 函数不返回任何内容，因此你无法进行检查。你可能想尝试使用我的 nVennR 包。目前该包在 CRAN 上不可用，但你可以通过以下命令从 Github 安装它：devtools::install_github("vqf/nVennR")。以下是一个示例：
>library(nVennR)>myV <- plotVenn(list(set1=c(1, 2, 3), set2=c(2, 3, 4), set3=c(3, 4, 5, 'a', 'b'), set4=c(5, 6, 1, 4)))[![在此输入图片描述][1]][1]>getVennRegion(myV, c('set2', 'set3', 'set4'))[1] 4>getVennRegion(myV, c('set3'))[1] "a" "b">listVennRegions(myV)$`0, 0, 0, 1 (set4)`[1] 6$`0, 0, 1, 0 (set3)`[1] "a" "b"$`0, 0, 1, 1 (set3, set4)`[1] 5$`0, 1, 1, 1 (set2, set3, set4)`[1] 4$`1, 0, 0, 1 (set1, set4)`[1] 1$`1, 1, 0, 0 (set1, set2)`[1] 2$`1, 1, 1, 0 (set1, set2, set3)`[1] "3"你可以在 [vignette][2] 中找到更多示例。[1]: https://i.stack.imgur.com/i17x2.png[2]: https://mran.microsoft.com/snapshot/2022-01-07/web/packages/nVennR/vignettes/nVennR.html<details><summary>英文:</summary>I have had a look at the package source and I cannot see any documented function to extract the elements in a region. In fact, the `venn` function does not return anything, so there is nothing you can check.You might want to try my `nVennR` package for that. At this time it is not available in CRAN, but you can install it from Github with `devtools::install_github("vqf/nVennR")`. An example:>library(nVennR)>myV <- plotVenn(list(set1=c(1, 2, 3), set2=c(2, 3, 4), set3=c(3, 4, 5, 'a', 'b'), set4=c(5, 6, 1, 4)))[![enter image description here][1]][1]>getVennRegion(myV, c('set2', 'set3', 'set4'))[1] 4>getVennRegion(myV, c('set3'))[1] "a" "b">listVennRegions(myV)$`0, 0, 0, 1 (set4)`[1] 6$`0, 0, 1, 0 (set3)`[1] "a" "b"$`0, 0, 1, 1 (set3, set4)`[1] 5$`0, 1, 1, 1 (set2, set3, set4)`[1] 4$`1, 0, 0, 1 (set1, set4)`[1] 1$`1, 1, 0, 0 (set1, set2)`[1] 2$`1, 1, 1, 0 (set1, set2, set3)`[1] "3"You can see more examples at the [vignette][2].[1]: https://i.stack.imgur.com/i17x2.png[2]: https://mran.microsoft.com/snapshot/2022-01-07/web/packages/nVennR/vignettes/nVennR.html</details>
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