使用VennDiagram包繪制韋恩圖
加載所需R包
library(VennDiagram)
# 設(shè)置工作路徑
setwd("/Users/Davey/Desktop/VennDiagram/")
# 清除當(dāng)前環(huán)境中的變量
rm(list=ls())
# 讀取測試數(shù)據(jù)
data = read.table("each_species_orthogroups.txt",header = T,sep="\t")
head(data)
AT Scaffold VIT Potri LOC_Os NC Gb Mapoly Phpat Smo Sphfalx kfl
1 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000 OG0000000
2 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001 OG0000001
3 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002 OG0000002
4 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000003 OG0000004
5 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000004 OG0000005
6 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000005 OG0000006
Cre Vocar
1 OG0000000 OG0000000
2 OG0000001 OG0000001
3 OG0000002 OG0000002
4 OG0000004 OG0000005
5 OG0000005 OG0000006
6 OG0000006 OG0000008
繪制一維韋恩圖
# 讀入數(shù)據(jù)為list類型，默認(rèn)圖片保存為tiff格式
venn.plot <- venn.diagram(
x = list(AT=data$AT),
filename = "1single_Venn.tiff",
col = "black", #邊框顏色
lwd = 5, #邊框線寬度
fontface = "bold", #標(biāo)簽字體
fill = "grey", #填充色
alpha = 0.7, #透明度
cex = 4, #標(biāo)簽字體大小
cat.cex = 3, #類名字體大小
cat.fontface = "bold", #類名字體
margin = 0.04 #邊際距離
)
image.png
繪制二維韋恩圖
# imagetype參數(shù)設(shè)定圖片保存類型為png
venn.plot <- venn.diagram(
x = list(
AT = data$AT,
Smo = data$Smo
),
filename = "2double_Venn.png", imagetype = "png",
lwd = 3,
fill = c("cornflowerblue", "darkorchid1"),
alpha = 0.6,
label.col = "white",
cex = 1.5,
fontfamily = "serif",
fontface = "bold",
cat.col = c("cornflowerblue", "darkorchid1"),
cat.cex = 2,
cat.fontfamily = "serif",
cat.fontface = "bold",
margin = 0.05,
cat.dist = c(0.03, 0.03),
cat.pos = c(-20, 20)
)
2double_Venn.png
繪制三維韋恩圖
venn.plot <- venn.diagram(
x = list(
AT = data$AT,
VIT = data$VIT,
Potri = data$Potri
),
filename = "3triple_Venn.tiff",
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
)
image.png
繪制四維韋恩圖
venn.plot <- venn.diagram(
x = list(
AT = data$AT,
Os = data$LOC_Os,
Scaffold = data$Scaffold,
Phpat = data$Phpat
),
filename = "4quadruple_Venn.tiff",
col = "black",
lty = "dotted", #邊框線型改為"dotted"虛線
lwd = 3, # 邊框線的寬度
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 = 2.0,
fontfamily = "serif",
fontface = "bold",
cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
cat.cex = 1.8,
cat.fontface = "bold",
cat.fontfamily = "serif"
)
image.png
繪制五維韋恩圖
venn.plot <- venn.diagram(
list(AT=data$AT,VIT=data$VIT,Os=data$LOC_Os,NC=data$NC,Scaffold=data$Scaffold),
filename = "out5venn.tiff",
lty = "dotted",
lwd = 2,
col = "black", #"transparent",
fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
alpha = 0.60,
cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
cat.cex = 0.8,
cat.fontface = "bold",
margin = 0.07,
cex = 0.8
)
image.png
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] VennDiagram_1.6.20 futile.logger_1.4.3 circlize_0.4.4
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 compiler_3.5.1 formatR_1.5 tools_3.5.1 GlobalOptions_0.1.0
[6] lambda.r_1.2.3 futile.options_1.0.1 shape_1.4.4
