r - 重叠两个基因集，找到它们的重叠意义并绘制它们

Question

(Fig. 3a, b, Extended Data Fig. 3a, b and Supplementary Table 1).After 48 h, more than one-third of the transcriptome wasdifferentially expressed (>5,000 genes; 405 genes encoding forproteins in the extracellular region, Gene Ontology (GO) accession0005576), significantly overlapping with the gene expression changesof A375 tumours in vivo after 5 days of vemurafenib treatment (Fig.3a, b and Extended Data Fig. 3c). Similar extensive gene expressionchanges were observed in Colo800 and UACC62 melanoma cells treatedwith vemurafenib and H3122 lung adenocarcinoma cells treated withcrizotinib (Extended Data Fig. 3d). Despite different cell lineages,different oncogenic drivers, and different targeted therapies weobserved a significant overlap between the secretome of melanoma andlung adenocarcinoma cells (P < 9.11 × 10−5)

原文paper

我希望看到与图 f 类似的情况，它显示了交叉点和显着性重叠。为了实现这一点，我让这段代码一直工作到交集部分，但我不知道如何运行重要部分。

library(reshape2)
library(venneuler)
RNA_seq_cds <- read.csv("~/Downloads/RNA_seq_gene_set.txt", header=TRUE, sep="\t")
head(RNA_seq_cds)
ATAC_seq <- read.csv("~/Downloads/ATAC_seq_gene_set.txt", header=TRUE, sep="\t")
head(ATAC_seq)
RNA_seq <- RNA_seq_cds
ATAC_seq <- ATAC_seq

#https://stackoverflow.com/questions/6988184/combining-two-data-frames-of-different-lengths
cbindPad <- function(...) {
  args <- list(...)
  n <- sapply(args, nrow)
  mx <- max(n)
  pad <- function(x, mx) {
    if (nrow(x) < mx) {
      nms <- colnames(x)
      padTemp <- matrix(NA, mx - nrow(x), ncol(x))
      colnames(padTemp) <- nms
      if (ncol(x) == 0) {
        return(padTemp)
      } else {
        return(rbind(x, padTemp))
      }
    } else {
      return(x)
    }
  }
  rs <- lapply(args, pad, mx)
  return(do.call(cbind, rs))
}

dat <- cbindPad(ATAC_seq, RNA_seq)

vennfun <- function(x) { 
  x$id <- seq(1, nrow(x))  #add a column of numbers (required for melt)
  xm <- melt(x, id.vars="id", na.rm=TRUE)  #melt table into two columns (value & variable)
  xc <- dcast(xm, value~variable, fun.aggregate=length)  #remove NA's, list presence/absence of each value for each variable (1 or 0)
  rownames(xc) <- xc$value  #value column=rownames (required for Venneuler)
  xc$value <- NULL  #remove redundent value column
  xc  #output the new dataframe
}

#https://stackoverflow.com/questions/9121956/legend-venn-diagram-in-venneuler
VennDat <- vennfun(dat)
genes.venn <- venneuler(VennDat)
genes.venn$labels <- c("RNA", "\nATAC" )
# plot(genes.venn, cex =15, )
#https://stackoverflow.com/questions/30225151/how-to-create-venn-diagram-in-r-studio-from-group-of-three-frequency-column
#https://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html   
vd <- venneuler(VennDat)
vd$labels <- paste(genes.venn$labels, colSums(VennDat))
plot(vd, cex=10)
text(.3, .45, 
     bquote(bold("Common ="~.(as.character(sum(rowSums(VennDat) == 2))))), 
     col="red", cex=1)

LABS <- vd$labels

上面的代码给出了交集图

现在是重要性部分，我如何在两个基因集之间做到这一点，并如原图所示显示它。

我的 data我用它来生成上面的图

如有任何建议或帮助，我们将不胜感激。

Answer 1

如果您谈论如何在图形下方放置任何文本，只需像以前一样使用“文本”。这只是对 x= 和 y= 坐标的一些猜测。 xpd=TRUE 允许您在边距上绘图。

VennDat <- vennfun(dat)
vd <- venneuler(VennDat)
vd$labels <- paste(c("RNA", "ATAC"), colSums(VennDat))

plot(vd, cex=10, border=c(NA, 'red'), col=c('#6b65af', '#ad7261'))
text(x=.5, y=.5, sum(rowSums(VennDat) == 2), xpd=TRUE)
text(.5, .15, 'overlap\n', xpd=TRUE)
text(.5, .13, bquote(italic(p)*'< 9.11E-55'), xpd=TRUE)

我还调整了plot的一些参数。您可以使用以下方法检查绘图方法的代码:

venneuler:::plot.VennDiagram

如果您想知道重要性是如何计算的，您应该在 Cross Validated 上发布您的问题。 .