#venn plot
rm(list = ls())
#############################################################1.1 input data
dir_path <- "C:\\Users\\liyix\\OneDrive\\Desktop\\"
dir_path_name <- dir(dir_path,pattern = "*.txt",full.names = T)
dir_path_name
## [1] "C:\\Users\\liyix\\OneDrive\\Desktop\\AB.txt"
## [2] "C:\\Users\\liyix\\OneDrive\\Desktop\\鏂板缓鏂囨湰鏂囨。.txt"
data_1 <- read.delim(grep("AB.txt",dir_path_name,value = T),header = T,stringsAsFactors = F)
head(data_1)
## Mapping.ID A B
## 1 OIRAEJWYWSAQNG 0 0
## 2 ZZQMUJGZCZTLQD 0 0
## 3 TWVUMMQUXMYOOH 0 0
## 4 GEDPQKGMHLHFOZ 0 0
## 5 GUIBJJJLGSYNKE 0 0
## 6 TUOSYWCFRFNJBS 0 0
dim(data_1) #[1] 1818 3
## [1] 1818 3
#A
data_1$A[data_1$A == 1] <- "AL inhibitor"
data_1$A[data_1$A == 0] <- "AL non-inhibitor"
##B
data_1$B[data_1$B == 1] <- "BB inhibitor"
data_1$B[data_1$B == 0] <- "BB non-inhibitor"
########################
data_3 <- data_1
head(data_3)
## Mapping.ID A B
## 1 OIRAEJWYWSAQNG AL non-inhibitor BB non-inhibitor
## 2 ZZQMUJGZCZTLQD AL non-inhibitor BB non-inhibitor
## 3 TWVUMMQUXMYOOH AL non-inhibitor BB non-inhibitor
## 4 GEDPQKGMHLHFOZ AL non-inhibitor BB non-inhibitor
## 5 GUIBJJJLGSYNKE AL non-inhibitor BB non-inhibitor
## 6 TUOSYWCFRFNJBS AL non-inhibitor BB non-inhibitor
library(VennDiagram)
## Loading required package: grid
## Loading required package: futile.logger
out_dir <- dir_path
p <- venn.diagram(list("AL inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$A == "AL inhibitor"])),
"AL non-inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$A == "AL non-inhibitor"])),
"BB inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$B == "BB inhibitor"])),
"BB non-inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$B == "BB non-inhibitor"]))),
filename = paste0(out_dir, Sys.Date(),"_VENN_PLOT",".tiff"),
counts = TRUE,lwd = 1.5,fontfamily = "sans",cat.fontfamily = "sans",
cat.col = c("darkblue", "darkred", "#e6b800", "darkgreen"),
col = c("darkblue", "darkred", "#e6b800", "darkgreen"),
fill = NULL,
alpha = 0.5,cat.fontface = 1,lty =1,margin = 0.05,
cex = 1,height = 2500, width = 2500,
fontface =1)
#########################################################output data
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
x <- list("AL inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$A == "AL inhibitor"])),
"AL non-inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$A == "AL non-inhibitor"])),
"BB inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$B == "BB inhibitor"])),
"BB non-inhibitor" = unique(na.omit(data_3$Mapping.ID[data_3$B == "BB non-inhibitor"])))
y <- x
ItemsList <- gplots::venn(x, show.plot = T,small=0.7)
ItemsList_1 <- attr(ItemsList, "intersections")
length(ItemsList_1) #[1] 4
## [1] 4
names(ItemsList_1)
## [1] "AL inhibitor:BB inhibitor" "AL inhibitor:BB non-inhibitor"
## [3] "AL non-inhibitor:BB inhibitor" "AL non-inhibitor:BB non-inhibitor"
for (i in 1:length(ItemsList_1)) {
#i =2
print(gsub(" \n ","-",names(ItemsList_1)[i]))
data_1 <- ItemsList_1[[names(ItemsList_1)[i]]]
data_2 <- data.frame(data_1)
data_2$source <- paste0(gsub(":","_",gsub(" \n ","-",names(ItemsList_1)[i])),"-",length(data_1))
write.csv(data_2,paste0(dir_path,Sys.Date(),"_",gsub(":","_",gsub(" \n ","-",names(ItemsList_1)[i])),"-",length(data_1),".csv"),row.names = F)
}
## [1] "AL inhibitor:BB inhibitor"
## [1] "AL inhibitor:BB non-inhibitor"
## [1] "AL non-inhibitor:BB inhibitor"
## [1] "AL non-inhibitor:BB non-inhibitor"
#####################method_2
#five sets Venn diagrams
#install.packages("venn")
library(venn)
##
## Attaching package: 'venn'
## The following object is masked from 'package:gplots':
##
## venn
library(ggplot2)
set.seed(12345)
x <- as.data.frame(matrix(sample(0:1, 100, replace = TRUE), ncol = 5))
x
## V1 V2 V3 V4 V5
## 1 1 1 1 0 1
## 2 0 0 1 1 0
## 3 1 1 1 1 0
## 4 1 1 1 0 1
## 5 1 0 0 0 0
## 6 1 1 1 0 0
## 7 1 1 0 0 0
## 8 0 1 1 0 1
## 9 0 1 0 0 0
## 10 1 1 1 1 0
## 11 1 0 1 1 0
## 12 1 0 0 0 0
## 13 1 1 1 0 1
## 14 0 0 0 1 0
## 15 1 1 0 0 1
## 16 0 1 0 1 1
## 17 1 1 0 1 1
## 18 1 0 0 1 0
## 19 0 1 0 0 1
## 20 1 1 0 0 1
venn::venn(x,ellipse = F,ilab=TRUE, zcolor = "style")
venn::venn(y,
color = c("darkblue", "darkred", "#e6b800", "darkgreen"),box = F, size = 0.5,
ggplot = T) +
annotate(geom="text", x= 500, y= 900, label= "venn package",
color="black")
ggsave(filename = paste0(Sys.Date(),"-venn package",".tif"),
plot = last_plot(),
device = "tiff", path = out_dir,
scale = 1, compression = "lzw", width = 8, height = 8, units = "cm",
dpi = 300, limitsize = TRUE)
###################### sample five-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,
B = B,
C = C,
D = D,
E = E
),
filename = "Venn_5set_pretty.tiff",
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
)