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利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）

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利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）最近对利用R绘制venn图进行了一些学习。参考了网上很多资料：【R作图】在R中绘制韦恩图的几种方法和一些漂亮的venn图如何使用R来绘制韦恩图（VennDiagram）venn.diagram:MakeaVennDiagram具体包括下面三个包：limma、venneuler、VennDiagram。总的来说，三个包都有着各自的不足。下面会一一进行说明，这里先放上结论：…

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最近对利用R绘制venn图进行了一些学习。参考了网上很多资料：

  1. 【R作图】在R中绘制韦恩图的几种方法 和 一些漂亮的venn图
  2. 如何使用R来绘制韦恩图（Venn Diagram）
  3. venn.diagram: Make a Venn Diagram
  4. how to add legends and values in a Venn diagram using R (VennEuler package)?

另外再推荐一个在线绘制venn图的网站（除了广告较多都挺好的）：https://www.meta-chart.com/venn

具体包括下面三个包： limma、venneuler、VennDiagram。总的来说，三个包都有着各自的不足。下面会一一进行说明，这里先放上结论：综合方便程度以及函数的多样性而言，VennDiagram > venneuler > limma。

limma

首先针对limma包，输入下两行就可以直接进行安装：

source("http://www.bioconductor.org/biocLite.R")
biocLite("limma")

虽然只用输入两行，但是运行之后你就会发现，依赖包需要安装到地老天荒，海枯石烂，花儿都谢了。（而且还可能安装失败）

（我们这里假设安装成功

之后利用vennDiagram()按照指定的用法就可进行venn图的绘制了，但这个包有一个很大的局限，就是最多只能够绘制3个集合，一旦超过就无法继续绘制了，而且绘制的效果也比较丑，如下所示。（由于实在没有安装成功，这里参考了网址：venn: Venn Diagrams）
利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）
实在不符合审美，我们进入下一个包。

venneuler

接着是venneuler，这个包绘制出来的图案就比上一个包要漂亮了许多，如下图所示：

vd <- venneuler(c(A=0.3, B=0.3, C=1.1, "A&C"=0.2, "B&C"=0.1 ,"A&B&C"=0.08))
plot(vd)

利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）

这个包也是存在缺点的，首先可能由于自己的水平没有到家，并不知道如何在集合上面显示数字。

为了克服第一个问题，在集合上面显示数字，我们可以用下面这个包——eulerr。

eulerr

这个包可以显示数字或者比例（quantities），并且可以自定义边框（edges），颜色（fills）等等。但还是没解决一个问题，如下图所示，A与B应该是没有交集，不应该重合在一起，但用代码绘制后使其有了交集

library(eulerr)

vd <- euler(c(A = 0.3, B = 0.3, C = 1.1,
              "A&B" = 0, "A&C" = 0.2, "B&C" = 0.1,
              "A&B&C" = 0.1))
plot(vd,
     fills = list(fill = c("#fbb4ae", "#b3cde3", "#ccebc5"), alpha = 0.6),
     labels = list(col = "white", font = 4), 
     edges = FALSE,
     quantities = TRUE)

利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）

VennDiagram

最后是VennDiagram，这个包功能非常完善，没有交集就不会重合，网上关于其的博客也是最多的。其绘制出来的图也可以非常美观

虽然这个包功能相对完善，但也有着其缺点，就是每个圈不会随着集合中数量的增大而增大，反映不出每个集合的相对大小。不过即使有这样的缺点，现在能搜索到的资源当中，比较丰富的就是这个包了。

下面的这些图都是VennDiagram绘制出来的~

搬运工

由于说明文档：venn.diagram: Make a Venn Diagram 中只有代码，没有每段代码输出的结果与其直接对应。这里我做一只勤劳的小蜜蜂，把运行的结果全部贴上来，便于之后查找以及DIY。

先放上汇总效果图：
利用R绘制venn图（VennDiagram、eulerr、venneuler、limma）

具体实现

首先载入函数包并设置路径，然后全部运行就可以将所有图片全部进行输出了。（这里不将所有的图贴上来，因为贴上来的图总是图裂显示不出来，所以只是将代码copy过来，具体可以自己运行参照着语句进行对比）

setwd('D:\\Pictures\\Blog\\venn')
library(VennDiagram)

# Note: most examples are listed as dontrun to meet CRAN requirements, 
# but all should work as-is!

# compact and minimal notation
## Not run: 
venn.plot <- venn.diagram(
  list(A = 1:150, B = 121:170), 
  "Venn_2set_simple.jpeg"
);
venn.plot <- venn.diagram(
  list(A = 1:150, B = 121:170, C = 101:200), 
  "Venn_3set_simple.jpeg"
);

## End(Not run)

# a more elaborate two-set Venn diagram with title and subtitle
venn.plot <- venn.diagram(
  x = list(
    "A" = 1:100,
    "B" = 96:140
  ),
  filename = "Venn_2set_complex.jpeg",
  scaled = TRUE,
  ext.text = TRUE,
  ext.line.lwd = 2,
  ext.dist = -0.15,
  ext.length = 0.9,
  ext.pos = -4,
  inverted = TRUE,
  cex = 2.5,
  cat.cex = 2.5,
  rotation.degree = 45,
  main = "Complex Venn Diagram",
  sub = "Featuring: rotation and external lines",
  main.cex = 2,
  sub.cex = 1
);

## Not run: 
# sample three-set Euler diagram
venn.plot <- venn.diagram(
  x = list(
    "Num A" = paste("Num", 1:100),
    "Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
    "Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
  euler.d = TRUE,
  filename = "Euler_3set_simple.jpeg",
  cat.pos = c(-20, 0, 20),
  cat.dist = c(0.05, 0.05, 0.02),
  cex = 2.5,
  cat.cex = 2.5,
  reverse = TRUE
);

# sample three-set Euler diagram
venn.plot <- venn.diagram(
  x = list(
    A = c(1:10),
    B = c(11:90),
    C = c(81:90)
  ),
  euler.d = TRUE,
  filename = "Euler_3set_scaled.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = 0
);

## End(Not run)

# sample four-set Venn Diagram
A <- sample(1:1000, 400, replace = FALSE);
B <- sample(1:1000, 600, replace = FALSE);
C <- sample(1:1000, 350, replace = FALSE);
D <- sample(1:1000, 550, replace = FALSE);
E <- sample(1:1000, 375, replace = FALSE);

venn.plot <- venn.diagram(
  x = list(
    A = A,
    D = D,
    B = B,
    C = C
  ),
  filename = "Venn_4set_pretty.jpeg",
  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"),
  cex = 1.5,
  fontfamily = "serif",
  fontface = "bold",
  cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
  cat.cex = 1.5,
  cat.pos = 0,
  cat.dist = 0.07,
  cat.fontfamily = "serif",
  rotation.degree = 270,
  margin = 0.2
);

# sample five-set Venn Diagram
venn.plot <- venn.diagram(
  x = list(
    A = A,
    B = B,
    C = C,
    D = D,
    E = E
  ),
  filename = "Venn_5set_pretty.jpeg",
  col = "black",
  fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
  alpha = 0.50,
  cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8,
          1, 0.8, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
  cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
  cat.cex = 1.5,
  cat.fontface = "bold",
  margin = 0.05
);

# Complex three-way Venn with labels & sub-/super-scripts 
venn.plot <- venn.diagram(
  x = list(
    I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205, 
          206:220),
    II = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175, 
           176:180),
    III = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375, 
            376:405)
  ),
  category.names = c(
    expression( bold('A'['1: subscript']) ),
    expression( bold('B'^'2: going up') ),
    expression( paste(bold('C'^'3'), bold('X'['i' <= 'r'^'2']^'2') ) )
  ),
  filename = 'Fig3-1_triple_labels_sub_and_superscripts.jpeg',
  output = TRUE,
  height = 3000,
  width = 3000,
  resolution = 300,
  compression = 'lzw',
  units = 'px',
  lwd = 6,
  lty = 'blank',
  fill = c('yellow', 'purple', 'green'),
  cex = 3.5,
  fontface = "bold",
  fontfamily = "sans",
  cat.cex = 3,
  cat.fontface = "bold",
  cat.default.pos = "outer",
  cat.pos = c(-27, 27, 135),
  cat.dist = c(0.055, 0.055, 0.085),
  cat.fontfamily = "sans",
  rotation = 1
);

# Complex 3-way Venn using expressions
venn.plot <- venn.diagram(
  x = list(
    "Num A" = paste("Num", 1:100),
    "Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
    "Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
  category.names = c(
    expression( bold('A'['1']) ),
    expression( bold('A'['2']) ),
    expression( bold('A'['3']) )
  ),
  euler.d = TRUE,
  filename = "Fig3-2_Euler_3set_simple_with_subscripts.jpeg",
  cat.pos = c(-20, 0, 20),
  cat.dist = c(0.05, 0.05, 0.02),
  cex = 2.5,
  cat.cex = 2.5,
  reverse = TRUE
);

## Not run: 
# Example to print to screen
venn.plot <- venn.diagram(
  x = list(
    sample1 = c(1:40),
    sample2 = c(30:60)
  ),
  filename = NULL
);

# Save picture to non-jpeg file type
# currently working on adding this functionality directly into venn.diagram
venn.plot <- venn.diagram(
  x = list (
    A = 1:10,
    B = 6:25
  ),
  filename = NULL
);

jpeg("venn_jpeg.jpg");
grid.draw(venn.plot);
dev.off();


## End(Not run)

#dontrun-starts-here
### NB: All figures from the paper can be run, but are turned off from
### automatic execution to reduce burden on CRAN computing resources.
## Not run: 
# Figure 1A
venn.plot <- venn.diagram(
  x = list(
    Label = 1:100
  ),
  filename = "1A-single_Venn.jpeg",
  col = "black",
  lwd = 9,
  fontface = "bold",
  fill = "grey",
  alpha = 0.75,
  cex = 4,
  cat.cex = 3,
  cat.fontface = "bold",
);

# Figure 1B
venn.plot <- venn.diagram(
  x = list(
    X = 1:150,
    Y = 121:180
  ),
  filename = "1B-double_Venn.jpeg",
  lwd = 4,
  fill = c("cornflowerblue", "darkorchid1"),
  alpha = 0.75,
  label.col = "white",
  cex = 4,
  fontfamily = "serif",
  fontface = "bold",
  cat.col = c("cornflowerblue", "darkorchid1"),
  cat.cex = 3,
  cat.fontfamily = "serif",
  cat.fontface = "bold",
  cat.dist = c(0.03, 0.03),
  cat.pos = c(-20, 14)
);

# Figure 1C
venn.plot <- venn.diagram(
  x = list(
    R = c(1:70, 71:110, 111:120, 121:140),
    B = c(141:200, 71:110, 111:120, 201:230),
    G = c(231:280, 111:120, 121:140, 201:230)
  ),
  filename = "1C-triple_Venn.jpeg",
  col = "transparent",
  fill = c("red", "blue", "green"),
  alpha = 0.5,
  label.col = c("darkred", "white", "darkblue", "white",
                "white", "white", "darkgreen"),
  cex = 2.5,
  fontfamily = "serif",
  fontface = "bold",
  cat.default.pos = "text",
  cat.col = c("darkred", "darkblue", "darkgreen"),
  cat.cex = 2.5,
  cat.fontfamily = "serif",
  cat.dist = c(0.06, 0.06, 0.03),
  cat.pos = 0
);

# Figure 1D
venn.plot <- venn.diagram(
  x = list(
    I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205, 
          206:220),
    IV = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175, 
           176:180),
    II = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375, 
           376:405),
    III = c(406:475, 286:335, 106:140, 141:160, 166:175, 181:205, 336:375, 
            476:530)
  ),
  filename = "1D-quadruple_Venn.jpeg",
  col = "black",
  lty = "dotted",
  lwd = 4,
  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"),
  cex = 2.5,
  fontfamily = "serif",
  fontface = "bold",
  cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
  cat.cex = 2.5,
  cat.fontfamily = "serif"
);

# Figure 2-1
venn.plot <- venn.diagram(
  x = list(
    A = 1:105,
    B = 101:115
  ),
  filename = "2-1_special_case_ext-text.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = c(-20, 20),
  ext.line.lty = "dotted",
  ext.line.lwd = 2,
  ext.pos = 12,
  ext.dist = -0.12,
  ext.length = 0.85
);

# Figure 2-2
venn.plot <- venn.diagram(
  x = list(
    A = 1:100,
    B = 1:10
  ),
  filename = "2-2_special_case_pairwise-inclusion.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = 0
);

# Figure 2-3
venn.plot <- venn.diagram(
  x = list(
    A = 1:150,
    B = 151:250
  ),
  filename = "2-3_special_case_pairwise-exclusion.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = c(0, 0),
  cat.dist = 0.05
);

# Figure 2-4
venn.plot <- venn.diagram(
  x = list(
    A = c(1:50, 101:140, 141:160, 161:170),
    B = c(171:230, 101:140, 161:170, 291:320),
    C = c(141:160, 161:170, 291:320)
  ),
  filename = "2-4_triple_special_case-001.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.dist = c(0.05, 0.05, -0.1)
);

# Figure 2-5
venn.plot <- venn.diagram(
  x = list(
    A = c(1:100),
    B = c(61:70, 71:100),
    C = c(41:60, 61:70)
  ),
  filename = "2-5_triple_special_case-012AA.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = c(-25, 0, 30),
  cat.dist = c(0.05, 0.05, 0.02)
);

# Figure 2-6
venn.plot <- venn.diagram(
  x = list(
    A = c(1:90),
    B = c(1:25),
    C = c(1:5)
  ),
  filename = "2-6_triple_special_case-022AAAO.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = 0,
  cat.dist = c(0.03, 0.03, 0.01)
);

# Figure 2-7
venn.plot <- venn.diagram(
  x = list(
    A = c(1:20),
    B = c(21:80),
    C = c(81:210)
  ),
  filename = "2-7_triple_special_case-100.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.dist = 0.05
);

# Figure 2-8
venn.plot <- venn.diagram(
  x = list(
    A = c(1:80),
    B = c(41:150),
    C = c(71:100)
  ),
  filename = "2-8_triple_special_case-011A.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.dist = c(0.07, 0.07, 0.02),
  cat.pos = c(-20, 20, 20)
);

# Figure 2-9
venn.plot <- venn.diagram(
  x = list(
    A = c(1:10),
    B = c(11:90),
    C = c(81:90)
  ),
  filename = "2-9_triple_special_case-121AO.jpeg",
  cex = 2.5,
  cat.cex = 2.5,
  cat.pos = 0,
  cat.dist = c(0.04, 0.04, 0.02),
  reverse = TRUE
);

#dontrun-ends-here

## End(Not run)
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