维恩图用R？

Question

除了limma包之外,还有用于在R中进行维恩图的其他包装.

有人有提示吗？

这里有关于用limma包做维恩图的一些注意事项.

Answer 1

维恩图包装清单:

• bvenn

• colorfulVennPlot

• eVenn
• 文氏图
• Venneuler
• Vennerable:R-Forge,GitHub
• eulerr

Answer 2

R-forge上有 Vennerable包.

source("http://bioconductor.org/biocLite.R")
biocLite(c("graph", "RBGL", "gtools", "xtable"))
install.packages("Vennerable", repos="http://R-Forge.R-project.org")

Answer 3

如果您需要创建4/5套的维恩图,gplots包中的venn函数也很有用.

Answer 4

我使用了两个自定义函数.我对venndia的实现绘制了维恩图并返回A和B(和C)之间重叠的列表.请参阅下面的代码.

有了这些,你就可以

vd <- venndia(A=LETTERS[1:15], B=LETTERS[5:20], getdata=TRUE)

这将绘制和返回数据.你可以通过这样做来关闭返回数据

venndia(A=LETTERS[1:15], B=LETTERS[5:20])

因为默认情况下getdata为FALSE./丹尼尔

circle <- function(x, y, r, ...) {
    ang <- seq(0, 2*pi, length = 100)
    xx <- x + r * cos(ang)
    yy <- y + r * sin(ang)
    polygon(xx, yy, ...)
}

venndia <- function(A, B, C, getdata=FALSE, ...){
    cMissing <- missing(C)
    if(cMissing){ C <- c() }

    unionAB <- union(A, B)
    unionAC <- union(A, C)
    unionBC <- union(B, C)
    uniqueA <- setdiff(A, unionBC)
    uniqueB <- setdiff(B, unionAC)
    uniqueC <- setdiff(C, unionAB)
    intersAB <- setdiff(intersect(A, B), C)
    intersAC <- setdiff(intersect(A, C), B)
    intersBC <- setdiff(intersect(B, C), A)
    intersABC <- intersect(intersect(A, B), intersect(B, C))

    nA <- length(uniqueA)   
    nB <- length(uniqueB)
    nC <- length(uniqueC)

    nAB <- length(intersAB)
    nAC <- length(intersAC)
    nBC <- length(intersBC)

    nABC <- length(intersABC)   

    par(mar=c(2, 2, 0, 0))
    plot(-10, -10, ylim=c(0, 9), xlim=c(0, 9), axes=FALSE, ...)
    circle(x=3, y=6, r=3, col=rgb(1,0,0,.5), border=NA)
    circle(x=6, y=6, r=3, col=rgb(0,.5,.1,.5), border=NA)
    circle(x=4.5, y=3, r=3, col=rgb(0,0,1,.5), border=NA)

    text( x=c(1.2, 7.7, 4.5), y=c(7.8, 7.8, 0.8), c("A", "B", "C"), cex=3, col="gray90" )

    text(
        x=c(2, 7, 4.5, 4.5, 3, 6, 4.5), 
        y=c(7, 7, 2  , 7  , 4, 4, 5), 
        c(nA, nB, nC, nAB, nAC, nBC, nABC), 
        cex=2
    )

    if(getdata){
        list(A=uniqueA, B=uniqueB, C=uniqueC, 
            AB=intersAB , AC=intersAC , BC=intersBC , 
            ABC=intersABC
        )
    }
}

Answer 5

Duncan Murdoch有一个维恩包,不在CRAN上.(帽子提示Gabor Grothendieck)

您还可以在"统计软件期刊"中阅读相关内容.

Answer 6

这是非常晚的,但它可能对其他人寻找答案有用: VennDiagram,在这里 CRAN .

它允许多组(用​​于venn的四组,用于Euler图的3组),可自定义的颜色和字体,简单的语法以及最佳的圆形大小与数据集的大小成比例(至少在比较2个数据时)套).安装:

install.packages("VennDiagram")
library(VennDiagram)

对于使用Bioconductor的包,并与基因组坐标的工作,最近文氏图被执行的包ChIPpeakAnno(版本2.5.12),并允许基因组坐标,例如,芯片起峰漂亮交叉点.对于早期采用者,您可能需要安装开发包.

peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704),
    end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")),
    space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f"))

peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260),
    end = c(967869, 2011108, 2496920, 3076166, 3123470),
    names = c("t1", "t2", "t3", "t4", "t5")),
    space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a"))

makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), NameOfPeaks=c("TF1", "TF2","TF3", "TF4"),
     totalTest=100,useFeature=TRUE, main="Venn Diagram",
    col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
    alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"))