R语言可视化：韦恩图绘制

Posted 2021-04-18 bioinfomics

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09.韦恩图绘制

---

清除当前环境中的变量

rm(list=ls())

设置工作目录

setwd("C:/Users/Dell/Desktop/R_Plots/09venndiagram/")

gplots包绘制韦恩图

library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess

data <- read.table("demo1_venn.txt", header = T, sep = "	")
head(data)
## Set1 Set2 Set3 Set4 Set5
## 1 ZMIZ1 ADCY5 TNS1 TNS1 TNS1
## 2 TNS1 ACTN4 ZMIZ1 ZMIZ1 ZMIZ1
## 3 CASZ1 SORBS1 RXRA RXRA TSPAN9
## 4 NFIC TNS1 AHDC1 NCOR2 MIDN
## 5 CACNA1C ZMIZ1 ACTN4 MIDN NCOR2
## 6 AHDC1 RBM20 MIDN AHDC1 AHDC1
attach(data)

# 绘制二维韦恩图
venn(data = list(Set1,Set2))

# 绘制三维韦恩图
venn(data = list(Set1,Set2,Set3))

# 绘制四维韦恩图
venn(data = list(Set1,Set2,Set3,Set4))

# 绘制五维韦恩图
venn(data = list(Set1,Set2,Set3,Set4,Set5))

VennDiagram包绘制韦恩图

library(VennDiagram)
## Loading required package: grid
## Loading required package: futile.logger

# 使用draw.single.venn函数绘制一维韦恩图
venn.plot <- draw.single.venn(
 area = 365,
 category = "All
Days",
 lwd = 5,
 lty = "blank",
 cex = 3,
 label.col = "orange",
 cat.cex = 4,
 cat.pos = 180,
 cat.dist = -0.20,
 cat.col = "white",
 fill = "red",
 alpha = 0.15
);
grid.newpage();

# 使用draw.pairwise.vennh函数绘制二维韦恩图
venn.plot <- draw.pairwise.venn(
 area1 = 100,
 area2 = 70,
 cross.area = 68,
 category = c("First", "Second"),
 fill = c("blue", "red"),
 lty = "blank",
 cex = 2,
 cat.cex = 2,
 cat.pos = c(285, 105),
 cat.dist = 0.09,
 cat.just = list(c(-1, -1), c(1, 1)),
 ext.pos = 30,
 ext.dist = -0.05,
 ext.length = 0.85,
 ext.line.lwd = 2,
 ext.line.lty = "dashed"
);
grid.newpage();

# 使用draw.triple.vennh函数绘制三维韦恩图
venn.plot <- draw.triple.venn(
 area1 = 65,
 area2 = 75,
 area3 = 85,
 n12 = 35,
 n23 = 15,
 n13 = 25,
 n123 = 5,
 category = c("First", "Second", "Third"),
 fill = c("blue", "red", "green"),
 lty = "blank",
 cex = 2,
 cat.cex = 2,
 cat.col = c("blue", "red", "green")
);
grid.newpage();

# 使用draw.quad.venn函数绘制四维韦恩图
# Reference four-set diagram
venn.plot <- draw.quad.venn(
 area1 = 72,
 area2 = 86,
 area3 = 50,
 area4 = 52,
 n12 = 44,
 n13 = 27,
 n14 = 32,
 n23 = 38,
 n24 = 32,
 n34 = 20,
 n123 = 18,
 n124 = 17,
 n134 = 11,
 n234 = 13,
 n1234 = 6,
 category = c("First", "Second", "Third", "Fourth"),
 fill = c("orange", "red", "green", "blue"),
 lty = "dashed",
 cex = 2,
 cat.cex = 2,
 cat.col = c("orange", "red", "green", "blue")
);
grid.newpage();

# 使用draw.quintuple.venn函数绘制五维韦恩图
# Reference five-set diagram
venn.plot <- draw.quintuple.venn(
 area1 = 301,
 area2 = 321,
 area3 = 311,
 area4 = 321,
 area5 = 301,
 n12 = 188,
 n13 = 191,
 n14 = 184,
 n15 = 177,
 n23 = 194,
 n24 = 197,
 n25 = 190,
 n34 = 190,
 n35 = 173,
 n45 = 186,
 n123 = 112,
 n124 = 108,
 n125 = 108,
 n134 = 111,
 n135 = 104,
 n145 = 104,
 n234 = 111,
 n235 = 107,
 n245 = 110,
 n345 = 100,
 n1234 = 61,
 n1235 = 60,
 n1245 = 59,
 n1345 = 58,
 n2345 = 57,
 n12345 = 31,
 category = c("A", "B", "C", "D", "E"),
 fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
 cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
 cat.cex = 2,
 margin = 0.05,
 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),
 ind = TRUE
);
grid.newpage();

# Writing to file
tiff(filename = "Quintuple_Venn_diagram.tiff", compression = "lzw");
grid.draw(venn.plot);
dev.off();

# 使用venn.diagram函数绘制韦恩图
data <- read.table("demo1_venn.txt", header = T, sep = "	")
head(data)
## Set1 Set2 Set3 Set4 Set5
## 1 ZMIZ1 ADCY5 TNS1 TNS1 TNS1
## 2 TNS1 ACTN4 ZMIZ1 ZMIZ1 ZMIZ1
## 3 CASZ1 SORBS1 RXRA RXRA TSPAN9
## 4 NFIC TNS1 AHDC1 NCOR2 MIDN
## 5 CACNA1C ZMIZ1 ACTN4 MIDN NCOR2
## 6 AHDC1 RBM20 MIDN AHDC1 AHDC1

attach(data)
## The following objects are masked from data (pos = 6):
##
## Set1, Set2, Set3, Set4, Set5

# 一维韦恩图
venn.plot <- venn.diagram(
  x = list(Set1=Set1),
  filename = NULL,
  col = "black",
  lwd = 9,
  fontface = "bold",
  fill = "grey",
  alpha = 0.75,
  cex = 4,
  cat.cex = 3,
  cat.fontface = "bold",
);
grid.draw(venn.plot);
grid.newpage();

# 二维韦恩图
venn.plot <- venn.diagram(
 x = list(Set1=Set1,Set2=Set2),
 filename = NULL,
 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)
);
grid.draw(venn.plot);
grid.newpage();

# 三维韦恩图
venn.plot <- venn.diagram(
  x = list(Set1=Set1,Set2=Set2,Set3=Set3),
  filename = NULL,
  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
);
grid.draw(venn.plot);
grid.newpage();

# 四维韦恩图
venn.plot <- venn.diagram(
  x = list(Set1=Set1,Set2=Set2,Set3=Set3,Set4=Set4),
  filename = NULL,
  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"
);
grid.draw(venn.plot);
grid.newpage();

# 五维韦恩图
venn.plot <- venn.diagram(
  x = list(Set1=Set1,Set2=Set2,Set3=Set3,Set4=Set4,Set5=Set5),
  filename = NULL,
  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
);
grid.draw(venn.plot);
grid.newpage();

sessionInfo()
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18363)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936
## [2] LC_CTYPE=Chinese (Simplified)_China.936
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C
## [5] LC_TIME=Chinese (Simplified)_China.936
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] VennDiagram_1.6.20 futile.logger_1.4.3 gplots_3.0.1.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.1 gtools_3.8.1 digest_0.6.20
## [4] bitops_1.0-6 futile.options_1.0.1 formatR_1.7
## [7] magrittr_1.5 evaluate_0.14 KernSmooth_2.23-15
## [10] stringi_1.4.3 gdata_2.18.0 rmarkdown_1.13
## [13] lambda.r_1.2.3 tools_3.6.0 stringr_1.4.0
## [16] xfun_0.8 yaml_2.2.0 compiler_3.6.0
## [19] caTools_1.17.1.2 htmltools_0.3.6 knitr_1.23

END

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