R语言绘制维恩图

Sat, 27 Aug 2011 00:00:00 +0000

很久之前整理的关于R绘制维恩图的资料，虽然，用R绘制维恩图并不是很常见，还是记下一笔，以备需要者参考。

# Gplots包
library(gplots)

## 
## 载入程序包：'gplots'

## The following object is masked from 'package:stats':
## 
## lowess

A<- 1:20
B<- 1:20
C<- 2:20
D<- 3:21

input<-list(A,B,C,D)
input

## [[1]]
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 
## [[2]]
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 
## [[3]]
## [1] 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 
## [[4]]
## [1] 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

venn(input)

A<- as.logical(rbinom(100, 1, 0.2))
B<- as.logical(rbinom(100, 1, 0.7))
C<- as.logical(rbinom(100, 1, 0.2))
D<- as.logical(rbinom(100, 1, 0.1))

input<-data.frame(A,B,C,D)
venn(input)

tmp <- venn(input, simplify=TRUE)

## Warning in drawVennDiagram(data = counts, small = small, showSetLogicLabel = showSetLogicLabel, : Not shown: 0101 contains 2

tmp

## num A B C D
## 0000 0 0 0 0 0
## 0001 1 0 0 0 1
## 0010 4 0 0 1 0
## 0011 0 0 0 1 1
## 0100 36 0 1 0 0
## 0101 2 0 1 0 1
## 0110 6 0 1 1 0
## 0111 1 0 1 1 1
## 1000 5 1 0 0 0
## 1001 0 1 0 0 1
## 1010 0 1 0 1 0
## 1011 1 1 0 1 1
## 1100 15 1 1 0 0
## 1101 1 1 1 0 1
## 1110 6 1 1 1 0
## 1111 1 1 1 1 1
## attr(,"intersections")
## attr(,"intersections")$A
## [1] "18" "29" "32" "54" "58"
## 
## attr(,"intersections")$B
## [1] "12" "14" "19" "22" "28" "30" "34" "36" "40" "43" "45" "46" 
## [13] "51" "52" "53" "57" "60" "66" "67" "68" "69" "70" "73" "75" 
## [25] "76" "77" "78" "80" "81" "87" "88" "89" "92" "94" "98" "100"
## 
## attr(,"intersections")$C
## [1] "6" "10" "33" "84"
## 
## attr(,"intersections")$D
## [1] "79"
## 
## attr(,"intersections")$`A:B`
## [1] "2" "5" "9" "13" "17" "21" "25" "26" "27" "38" "39" "44" "49" "50" "56"
## 
## attr(,"intersections")$`B:C`
## [1] "20" "71" "72" "82" "83" "97"
## 
## attr(,"intersections")$`B:D`
## [1] "62" "63"
## 
## attr(,"intersections")$`A:B:C`
## [1] "3" "11" "47" "74" "85" "95"
## 
## attr(,"intersections")$`A:B:D`
## [1] "96"
## 
## attr(,"intersections")$`A:C:D`
## [1] "7"
## 
## attr(,"intersections")$`B:C:D`
## [1] "23"
## 
## attr(,"intersections")$`A:B:C:D`
## [1] "37"
## 
## attr(,"class")
## [1] "venn"

venn(input, showSetLogicLabel=TRUE)

# asbio包
library(asbio)

## 载入需要的程序包：tcltk

Venn(A=.3,B=.2,AandB=.06)

# limma包
# install.packages("BiocManager")
# BiocManager::install("limma")
library(limma)
Y <- matrix(rnorm(100*6),100,6)
Y[1:10,3:4] <- Y[1:10,3:4]+3
Y[1:20,5:6] <- Y[1:20,5:6]+3
design <- cbind(1,c(0,0,1,1,0,0),c(0,0,0,0,1,1))
fit <- eBayes(lmFit(Y,design))
results <- decideTests(fit)
a <- vennCounts(results)
print(a)

## x1 x2 x3 Counts
## 1 0 0 0 88
## 2 0 0 1 8
## 3 0 1 0 0
## 4 0 1 1 4
## 5 1 0 0 0
## 6 1 0 1 0
## 7 1 1 0 0
## 8 1 1 1 0
## attr(,"class")
## [1] "VennCounts"

vennDiagram(a)

vennDiagram(results,include=c("up","down"),counts.col=c("red","green"))

# venneuler包

library(venneuler)

## 载入需要的程序包：rJava

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

plot(vd)

m <- data.frame(elements=c("1","2","2","2","3"),sets=c("A","A","B","C","C"))
 
v <- venneuler(m)

plot(v)

m <- as.matrix(data.frame(A=c(1.5, 0.2, 0.4, 0, 0),B=c(0, 0.2, 0, 1, 0), C=c(0, 0, 0.3, 0, 1)))

v <- venneuler(m > 0)

plot(v)

v <- venneuler(m)

plot(v)

# Vennerable包

# BiocManager::install("graph")
# BiocManager::install("RBGL")
# BiocManager::install("reshape")
# install.packages("Vennerable", repos="http://R-Forge.R-project.org")

library(Vennerable)

## 载入需要的程序包：graph

## 载入需要的程序包：BiocGenerics

## 载入需要的程序包：generics

## 
## 载入程序包：'generics'

## The following objects are masked from 'package:base':
## 
## as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
## setequal, union

## 
## 载入程序包：'BiocGenerics'

## The following objects are masked from 'package:rJava':
## 
## anyDuplicated, duplicated, unique

## The following object is masked from 'package:limma':
## 
## plotMA

## The following objects are masked from 'package:stats':
## 
## IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique,
## unsplit, which.max, which.min

## 载入需要的程序包：RBGL

## 载入需要的程序包：grid

## 载入需要的程序包：lattice

## 载入需要的程序包：RColorBrewer

## 载入需要的程序包：reshape

## 载入需要的程序包：gtools

## 载入需要的程序包：xtable

## 
## 载入程序包：'Vennerable'

## The following object is masked from 'package:asbio':
## 
## Venn

Venn(n=3)

## A Venn object on 3 sets named
## 1,2,3 
## 000 100 010 110 001 101 011 111 
## 1 1 1 1 1 1 1 1

plot(Venn(n=3))

data(StemCell)
w <- Venn(Sets=StemCell[1:2])
Weights(w)

## 00 10 01 11 
## 0 219 875 404

plot(w)

Weights(w) <- 1:4
plot(w)

韦恩图 on 格物堂

R语言绘制维恩图