Gplots包

> library(gplots)

Loading required package: gtools

Loading required package: gdata

Attaching package: ‘gdata’

The following object(s) are masked from ‘package:utils’:

object.size

Loading required package: caTools

Loading required package: bitops

Loading required package: grid

Attaching package: ‘gplots’

The following object(s) are masked from ‘package:stats’:

lowess

> ##

> ## Example using a list of item indexes belonging to the

> ## specified group.

> ##

> 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)

> tmp

num A B C D

0000 0 0 0 0 0

0001 1 0 0 0 1

0010 1 0 0 1 0

0011 0 0 0 1 1

0100 38 0 1 0 0

0101 8 0 1 0 1

0110 12 0 1 1 0

0111 0 0 1 1 1

1000 4 1 0 0 0

1001 0 1 0 0 1

1010 1 1 0 1 0

1011 0 1 0 1 1

1100 13 1 1 0 0

1101 1 1 1 0 1

1110 3 1 1 1 0

1111 0 1 1 1 1

>venn(input, showSetLogicLabel=TRUE)

> venn(input, universe=NULL, showSetLogicLabel=TRUE)

asbio包

> library(asbio)

Loading required package: plotrix

Attaching package: ‘plotrix’

The following object(s) are masked from ‘package:gplots’:

plotCI

Loading required package: vegan

This is vegan 1.17-2

Attaching package: ‘vegan’

The following object(s) are masked from ‘package:gtools’

permute

Loading required package: MASS

Loading required package: lmomco

Package lmomco (0.97.4) loaded.

Loading required package: cluster

Loading required package: boot

Attaching package: ‘boot’

The following object(s) are masked from ‘package:gtools’:

inv.logit, logit

Loading required package: akima

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

limma包

> library(limma)

Warning message:

semi-transparency is not supported on this device: reported only once per page

> 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 87

[2,] 0 0 1 9

[3,] 0 1 0 2

[4,] 0 1 1 2

[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)

Loading required package: 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”))

Warning message:

semi-transparency is not supported on this device: reported only once per page

> 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)))

Warning message:

semi-transparency is not supported on this device: reported only once per page

> # without weights

> v <- venneuler(m > 0)

> plot(v)

> v <- venneuler(m)

> plot(v)

Vennerable包

> library(Vennerable)

Loading required package: graph

Loading required package: RBGL

Loading required package: lattice

Attaching package: ‘lattice’

The following object(s) are masked from ‘package:boot’:

melanoma

Loading required package: RColorBrewer

Loading required package: reshape

Loading required package: plyr

Attaching package: ‘Vennerable’

The following object(s) are 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)